Or maybe, just maybe, I'm looking for ways the flaws might be fixed and opinions on possible solutions. Nah, that's just too crazy.
In all the threads you've started, you asked a question and then told people who answered you that they were playing the game wrong. All those people have been playing a long time, and have solved various problems with their methods, including the one you are asking questions about. It's fine if you just don't like the game, and it's fine if you don't like the solutions that people propose. I don't like a lot of the solutions to any given problem either, so I use my own. That's how Fate works, anything that happens can be done in a number of ways, depending on the preferences of the players involved. That doesn't make any of those ways right or wrong. I would appreciate if you could keep that in mind when talking to people around here.
Fate doesn't try to simulate reality (or even a dresdenverse version of reality), it emulates narrative structures. It can be used to simulate things to a degree, but there are a lot of other systems that do that better, and you are always going to run into problems if you try to play it like that. Even more so, if you don't expect to run into those problems. It took me a while to get this, as well, and it's especially tough when coming from other, more traditional games.
Let's start with stress. Stress is not equal to hitpoints or health or however other games that have mechanics similar to this call it. Neither is mental stress equal to mana. In Fate, stress is used as a pacing mechanism. It takes a while to burn through someone's stress track, so it will make a conflict last longer. If a conflict is not interesting to me, I could resolve it as a single roll, the player and I both roll the fists skill for the characters involved, and the higher roll wins the entire conflict. But since the game is about action, I usually want my fights to last a bit longer, so I choose to use a mechanic that will last longer. The conflict is that mechanic.
But I might want to have something that lasts even longer. That's when I can simply reset the stress and treat what happens next as a new scene. Imagine a tv series with a big fight scene. Lots of action, people get hit, thrown against the wall, they hurt pretty bad. Then there's a moment of high suspension and suddenly, there's a commercial break.
And that's where the stress reset can set in. There doesn't have to be a reason like "the characters have a few minutes to catch their breath" or anything. It's a way to structure your narrative, and if you want the fight to keep going, just when it reaches its peak, go for it. Of course it should count for everyone, players and NPCs alike.
There's also another way to go here, and that's sub-goals. An important part of setting up a conflict is to set up a goal for each side, and they should be somewhat opposite. Most often, the goal is simply "kill the opposition", which is fine, but it isn't always the best choice. And sometimes, it might not even be a choice at all. Instead, and especially if you want to prolong your final fight scene, you can set up sub-goals. You basically need to take out your opponent a few times in a row, each time something happens. Maybe they lose an arm, their mythical weapon, the amulet that makes them immune to magic, whatever you've got. Once such a taken out has occurred, everything is reset, and the next conflict begins.
But again, the mechanical conflict only. It could be that you are literally mid karate chop when this happens, but that doesn't matter, there's been a break in the narrative, something has dramatically changed, that warrants a change of pace.
Next, plot devices. Let's go back to the situation where Harry opens a portal in the deeps to let Marcone in. I would handle this one of two ways:
1) The plan was hatched on-screen. The players anticipated that the deeps would be full of armed thugs, so they found a way to counter it, ask Marcone and his goons for help. The negotiation with Marcone was played out in full, and the situation was planned so that sometime in the deeps, Harry could simply "activate" Marcone to neutralize the thugs that would otherwise outnumber them. It was agreed upon that this would simply happen, there was no need for a spell or anything, it was just a plot device. When Harry's player said "now", Harry would open the portal and Marcone was there to the rescue. Harry would cast a spell to open the portal, obviously, but it was already decided that this would happen, so there was no need in rolling anything. The spell was just the plot device to get Marcone there, it was not a spell that Harry had to roll to control or anything like that. It was decided that this would be a cool thing to happen, so it happened.
2) In the middle of the deeps, Harry's player realizes that he is heavily outnumbered. He comes up with the idea that he could have gone to Marcone and asked him to lend him some of his goons. He didn't do that before going into the deeps, but the player hands the GM a Fate point and they agree that Harry has done that, and now they are waiting on the other side, ready to strike. Opening the portal is part of spending the Fate point, again there's no need to roll, it happens, because the player paid for it. It's a plot device, something that just happens, because the plot demands it to. You may think this is arbitrary, and to a degree you are right, but it is still under the scrutiny of the table, and if everything agrees that this is something cool that could happen, why stand in the way?
And if you ask other players, I'm sure they will find a few dozen other ways you could do this. Now obviously, you could ask Harry's player to roll to open the way, but I would advise against it. If you have something cool like this in the barrel, you'd sort of be shooting yourself in the foot, if you force a roll on it, since the roll can fail and you stand there with nothing. You can always go for a compel, if you want to twist things. Which is also something that happens there. Harry's plan was to escape through the portal with the rest. But he had probably spent all his Fate points already, and the GM grinned, held up a Fate point and said "Wouldn't it be a shame, if you were under a psychic attack and missed the closing portal by this much?" He can only accept and find another way out, which he did with Lara and the kiss-shield, probably also powered by the same Fate point he just got.
Speaking off, I had a plot device spell like that happen in my own game, and it's pretty much my favorite scene ever. The players were fighting the resurrection of the red king and had failed, he was standing in front of them. The Warden of the group (played by bobjob) charged him, set off his death curse while tapping into summer magic and exploded into a nova of pure sunshine, burning the red king and any red court vampire around to ashes.
Now I could have calculated how many shifts of power that would have been, and if it would have been enough to take out the red king, or if he survives, etc. But I ask you, why would I rob me and my players from an amazing ending like that? It worked, without asking, it worked. Sometimes, the rule of cool just trumps everything, at least in my opinion.
The difference between narrative and simulative is really where I'm coming from the entire time. A simulative approach means you will have to put everything that happens into rules and numbers. And that's well and good, but it's important you know that's what you are doing or that's what you are expecting from a game. The narrative approach on the other hand tries to be light on rules and only uses rules to form the narrative.
For example, when Harry goes into a dark room, he has two option: he can either switch on the light, or he can call forth light from his amulet. Now I'm not talking general, I'm talking this specific example. Since Harry is a wizard, it's kind of cool to have him use his magic to make light. The simulative approach would now say that since it is a spell, Harry would need to roll for it and take stress. The narrative approach would say that there is effectively no difference between switching on the light and magical light, both light up the room so Harry can see where he is and what's there. No need to roll for one, so there's no need to roll for the other, it's just this characters flavor. This flavor magic is actually in the book (YS259 - Mundane Effects)
Murphy might have brought a flashlight, which would be her style.
It's kind of like when you expect to drink coke and get sprite instead, it will simply taste wrong. If you drink the same sprite, expecting it to be sprite, it'll taste completely different.
And this is kind of why the rules seem so vague. It's because they are. But that's intended, because it's up to each group to figure out how they want to deal with things. The book gives a lot of examples and a lot of advice on how to do so, but ultimately, it leaves a lot of wiggle room for people to find their sweet spot. I can totally understand that this might not be to your liking, but maybe if you look at it from another angle, you might at least understand the intentions behind the rules. Then you can decide if this is the game for you, or if you might be better off with a game that better matches your style of playing.