Jim has stated that the beings of immense power (Gods, or whatever you want to call them) are pretty cool, and it's all of us who are stupid.  I take that comment to mean that there is basically one being in any given role, but there are tons of names and variations on what the role is which have been generated over time and associated with the being in such a way that the being has essentially absorbed those names and associations.  The being itself has not changed, but mortal perception and understanding of the being has, over time.  As an example, the Creator is one being, let's call him George.  George has always been around and always will be around and will forever do what he does.  Over time, different mortal civilizations have seen small bits of George and theorized different reasons for George's existence.  Some people called him God.  Some people called him Allah.  Others referred to Yahweh, or Jehovah, or Jesus, or The Light, or Elohim.  It doesn't matter, George is who he is and does what he does, and he forgives all the ignorant mortals that waste their time arguing and fighting wars over who is correct.

The point of this is, George is George is George.  Different groups of people, in different times, shaped by different geographic locations and languages and cultures have all described the same being in different ways.  This is significant, and George notices, but it doesn't change who he is or what he does.  The mortals just perceive him differently based on all these names and descriptions. 

George might, were he so inclined and able to appear to some civilization, utilize their particular perception of him in order to make the experience less shocking and more understandable.  George is George, but an American Roman Catholic doesn't know George.  So, if George was going to appear to this person he might appear as "God," because this person has a set of concepts associated with that theorized being that he would understand.  "God" is a very biased and incomplete picture of George, but at least it's a framework this person would understand, so George doesn't have to work from scratch to explain who he is to this person.

Now, take another being and do the same thing.  I'll call her Edna.  Greek & Roman culture in Harry Dresden's universe described Edna as Hecate.  Harry Dresden knows 6 Queens of Faerie.  Perhaps in his reality, mortal choices have been made throughout time that have resulted in a world where Edna is now perceived as 6 different, individual beings.  Edna is still who she's always been, doing what she's always done, but mortal perception and understanding of her has changed over time such that she interacts with mortals in this reality as 6 different beings, rather than as 3 or as just 1.  Edna doesn't really care HOW she gets her job done, just THAT she gets her job done.  It makes no difference to her if Harry and other mortals think there are 6 people doing 6 different jobs, at the end of the day it all adds up to Edna just doing her thing. 

You can think of it like a type of interface, really.  George and Edna are who they are and they've got Jobs to do.  They need mortal help to do these Jobs, to one degree or another.  George and Edna would destroy our reality by coming into it as themselves, so they use an interface to interact with us, rather than direct, face-to-face conversation.  They have a variety of different options to choose from, and they choose the appropriate interface for the particular mortals they are interacting with at the time.  Harry wouldn't understand many of the different perceptions of Edna that other civilizations throughout time or in different realities have described, so using those interfaces would make Edna's job more difficult.  It's simplest for her to use one (or all) of the Faerie Queens to interface with Harry, because he has the best understanding of Edna through those constructs, and Edna has less background work to do in order to get Harry's help.

This also explains, when the Mothers were talking about Harry's use of various Names to describe Mother Winter, why both Mothers were worried about him knowing one /particular/ Name.  Just as there are names and Names, I believe there are also NAMES!  Edna is the NAME of a particular being, and there might be many Names, each associated with small parts of that being.  Invoking one of those Names might get the attention of part of that being, but invoking the entire, full being's NAME is something orders of magnitude greater.

I don't know if I buy into the idea of beings on higher planes of existence flaking off bits of themselves every time mortal decisions are made and creating lower-tier beings.  It seems clear there are mechanisms that beings can move up or down these tiers, but I think it's more mechanical and less mystical.  I can buy that there was one Creator being that created many of the other powerful beings, but I think that's where it stopped, I don't think it's an ever-continuing process.  I think George created a lieutenant, Frank, to do a particular Job, and Frank's been doing that ever since, as different beings in different realities.  Frank didn't suddenly flake off of George as a mini-me because some mortal made a particular choice in a particular reality.  If that were the case, Frank wouldn't span all realities,  because the choice that spawned him in one reality would not have happened in every other reality.

Now, sometimes these other powerful beings that were created might go away for one reason or another (they Fell, retired, or are simply "Out"), but that's why there are mechanisms in place for other beings to gain power and ascend to higher planes of existence.  If they are worthy enough, and make the correct choices, they will figure it out and become what they need to become to take over some particular role that needs filled.  Remember, Mab wasn't created to guard the Outer Gates, and it wasn't always a Winter Queen that was in charge of that Job.  She started out as a mortal and eventually rose to her current position, and then took over that Job from some other being or group.  This wouldn't really be necessary if it were as simple and convenient as George flaking off a new guard of the Outer Gates when the right choice was made by some mortal.

Griff's construction is simpler to grasp, just because it skips a lot of the higher-level conceptualization and goes right into simple, real-world analogies.  I don't think these two ways of describing the cosmology are mutually exclusive, mind you, although they could be.  It depends on how you characterize each, but I think they could simply be two different ways of describing the same situation.

Under this model, Griff, I think it might be more accurate to describe reality-spanning beings as the soil, rather than the roots.  The tree roots might not all interconnect, but they do all grow in the same soil.  The Lieutenants like Frank are the soil that spans the entirety of the forest, but even they don't have the highest vantage point.  George, the Creator, is responsible for the light and rainfall that allow the trees to grow.  George gives Frank what he needs and Frank does his Job, as the soil.