I have the same questions as you on this !
Whilst the different PD models we have implemented generally do not take into account fatigue. The Extended Model looks at longer durations and then adjusts accordingly whilst the Veloclinic models have 3 different approaches for accounting for fatigue. So far the Extended Model will underestimate longer durations if you don't have any decent efforts of a longer duration where, with most of the data I have seen, the veloclinic models always seem to underestimate.
For intermittent exercise, my understanding is that W' bal will reflect depletion / reconstitution of W' and tau may or may not take fatigue over the ride into account, since it is computed by looking at the entire ride (but, I don't really know). Also, since slow-twitch muscles do not fatigue as quickly as fast twitch I expect that by the time you're sustainable power (reduced CP) has dropped due to muscular fatigue your W' has also gone anyway (Again, I am speculating).
Hydration and nutrition (bonking) I guess are assumed to be managed by the athlete ?
It would be so cool to identify rides that had impacted your ability to recover CP/W' during the ride (if that is even valid) -- and would they signal greater adaptations or fatigue systems so much they impeded post ride recovery (I have no idea).
We just need to wait for the clever guys researching this stuff to tell us !
Mark