first of all, thanks for the excellent post!

That diagram is really interesting, Im 40 and a cat 3 rider, not particularly good at any one thing, just an all round hacker really, so theyre all equally relevant. I think whats interesting like you say, is the wildly different rates for 'supercompensation', ranging from 12 hours, to 24 to well over 48. I suppose the only way to really try and factor it into any training programme would be to confirm what you said about each of the 3 suiting a particular type of effort, and then equate the 3 to your own relative efforts or training sessions.

example:
Glycogen - sprints - 1hr intense hill repeats / intervals (130ish tss) - repeat 1 day later
fitness Level (?) - 2-4 hour rolling (200ish tss) - repeat 1 / 2 days later
mitochondria - hard endurance - 4/5+ hour ride/race (+300ish tss) repeat 3 days later

I think the categories could do with clarifying a little also, the only clear one seems to be mitochondria recovery.
Glycogen: do you think this means Glycogen storage, use and replenishment (supercompensation would increase the store size perhaps)
Fitness Level: overall non-specific fitness level?

I'll continue to do some digging on this

Cheers