This is something I'd love to do. And I think I'm close to being able to. The stuff below is kind of relevant.
Now that I've learned how to use Conditional Activation Groups, I've got a very stupid version of GC-BTT that will switch to the stock Touch Bar only when a text area is in focus, enabling access to autocomplete and autofill. I've found that turning off Apple's Control Strip entirely makes the experience a bit less jarring. I'll refine this behavior and be VERY selective about ever booting out to the stock Touch Bar.
So, to bring things full circle, I plan to use conditional activation groups to basically turn the stock Touch Bar into a modal widget. That way apps with worthwhile Touch Bar controls (so, basically just Safari) will get through without disrupting the overall GC-BTT experience.
EDIT: That release is now live - GoldenChaos-BTT 2.670!
EDIT2: @Andreas_Hegenberg The progress bar visualization for reapplying settings has broken in 2.670 