(I’m asking this mostly for the VO2max workouts, but the question is more broadly applicable as well)
Most TR workouts are of the form “do N repeats of X minutes at Y% of FTP”, and I’m trying to contrast this against what I recently read in the Training+Racing with a Power Meter book by Hunter Allen et al.
In the book, they talk about “when to stop intervals”, which basically tries to find the optimum number of intervals one should do. So for example, with a 5 minute interval, they recommend (generally) stopping after your power in a given interval is less than 5-7% of your power in the 3rd interval. But if I’m following a TR workout that says, for example, 5 * 5 minutes at 110%, and I can still hold 108% at the end of the 5th interval, should I stop or should I keep going until I reach that prescribed 5-7% drop in power?
My interpretation of the ‘when to stop intervals’ guidance is that it isn’t to determine the optimal number of intervals to do or to add more intervals. Its to determine if continuing is unproductive because you cannot generate the desired power.
Following their guidance for your example, if you do the 5th interval at 108% I’d just stop because the planned workout is done. The box has been checked. If power of the 4th interval dropped to 100% I’d stop because I cannot do the desired power and its no longer a productive supra-threshold effort and then think about why I am having trouble with the workout (fueling? not recovered? bad sleep?) and try to fix it for the next workout.
This may or may not be the right answer but depending on how I’m feeling and if subsequent workouts within the next 4 days won’t be negatively impacted, if I have to bail out of intervals I’ll often just go into resistance mode and just cruise along at 60-65% for time of the original workout rather than just bailing entirely. Objectives of the high intensity work are mostly met but no reason to stop early unless you’re feeling pretty rough. IMO can never go wrong with more aerobic work 
unless it is going to inhibit your recovery with less sleep or other responsibilities