That sounds like the situational and plot based bonuses that either Stunts or aspect invocations would provide, depending on how often they'd come up.

So keep your skill at 0 and buy a bunch of stunts.

Your story really only reinforces the idea that the suggested mechanic only works if EVERYONE has one.

Perhaps the problem is the fact that compared to "vanilla" mortals, supernatural critters are already that--SUPERnatural.  They already have many things going for them against mundanes, because, c'mon--your "typical" RCV would inspire quite a LOT of fear in such people (and would give even elite soldiers a tough time).  We've been doing this for an even year now and have only now reached -11 Refresh point (we started at Chest-Deep). 

And now we feel we have to make the SUPERnaturals, well, even more SUPER.  Not necessary.  If your PC's are too powerful for you to make a worthy challenge for them, then you're either going to have to change your tactics or the style of the game you're running. 

By the way, what's with the High Refresh games?  Granted we only play about once or twice a month on average, but I'm happy with the pace of advance.  I'd rather have the journey to -14 Refresh than start there.

The Kerberos Club Skill rules almost seem like a replacement for the standard power system and that's how I'd use them. Want Inhuman Strength? Spend -2 and get 3DF+1D6 to your Fists and Might skill. Want to seduce someone like the White King? Spend -4 refresh and get 2DF+2D6 to your Presence and Deceit. A lot of the justification for the Supernaturalness (I made that word up) powers could be turned into Aspects to be tagged. Want to dish extra damage for sucking down some blood? Fate Point to tag Red Court Thug and roll your existing Inhuman Tier Fists skill. Want to Speak to the Dead? Tag Ectomancer Private Eye and roll your Tiered Alertness.

It would remove Pure Mortal as a concept since Pure Mortals would have access to Tiered skills as well. Just give them a Regular Joe Schmoe aspect and call it done. Alternately, you can come up with a way to make Pure Mortals different but still viable. I can't think of anyway off of the top of my head, but you could.

There would be some kinks to work out, but I think this would be doable. I'd remove Armor and Weapon values and go the Fate Core idea for Weapon and Armor are rolled into Skill rolls. Magic could bend the paradigm even further by still attacking the Mental Stress track and allowing you to use those skills in place of other things, but could be boiled down to a single dice roll at an Averaged Power level (I would go half of the maximum D6 plus half of the remaining DF for Rotes, everything non-Rote you're rolling for with much wilder results). Power would still go off of Conviction and Discipline for targeting. You'd just need to buy up Tier levels in the appropriate skills, which would also encompass Refinement.

Sancta is right, it will be a custom system, but you can build it using *most* of the existing rules.

Introducing the skill tiers makes them pretty much mandatory for every character that wishes to contribute in that field, though. If Player A plays a character with Weapons 5 and duels against an old vampire who has Weapons 5 and Strength powers, it's a tough but not unbeatable matchup that one can win with FP investment or the right implement (such as a holy/sword of the cross). Now, if the Vampire had Supernatural tier Weapons (which would totally fit, given its experience), Player A is not even going to try to fight without a similar tier of skill; any straight fight will see him facedown in the gutter and various orifices sodomized.

If you absolutely need to implement these powers, [-3] per tier seems about appropriate. Do note that these powers encourage an arms race mentality and are likely to become a power tax.