I will be completing my TR workouts in Zwift for the most part this winter. As AIFTP adjusts, I’ve found some workouts spot on (ie threshold) and others fairly easy or too short (is sweet spot). With the latter I will either add intervals or add endurance time. I don’t want to complete the cool down before continuing, so I end the formal workout and ride on. The issue is that I won’t get the survey in zwift, and in TR it gets marked as ending the workout early and I can’t rate the workout difficulty, instead being asked why I quit when I try to adjust it and just showing that reason as my response.It does seem to adjust the levels appropriately, but can/does it not just compare the work completed to the work assigned?
Have you tried ramping the intensity up to 125% during the cooldown? That will get you closer. Or you can turn off ERG and just ride ignoring the guidance for watts.
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I usually just click the next interval until workout is finished. I recall i have received the query even if i have continued with something outside of workout.
I do the 125% and then turn off erg to extend the ride after I earn all my stars. I’m embarrassed to admit how much I’m motivated by badges and levels.
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In this situation, I’d recommend using Workout Alternates to replace your scheduled workout with one from the “harder” or “longer” section, rather than adding unstructured volume. 
It’s likely going to be a better experience all around.