M,
This is a great question, really glad you asked it.
This issue is at the root of looking at the purpose of each workout. Each workout’s goal can be categorized into increasing General Fitness goal or Specific fitness goal (some workouts target both, but at a minimum, each workout segment is focused on one of these two categories).
Yes, TT position is going to generate less power than road position, and the aerodynamic tradeoff is always worth it. However, while 10-15 watts is a typical decrease in FTP in TT position, it’s different for each athlete. Can be as little as 5 and as much as 20.
So, the best option is to have an FTP tested in TT position and get your precise zones for TT.
Regarding the bike position when performing higher intensity intervals, it depends. If you are a Sprint or Oly athlete, a significant amount of your intervals should be done in TT, because that it the position you will race in (Specificity). If you are an IM or 70.3 athlete, you can maintain road position for all intervals, because you won’t be in TT position for Zone 3+ in your event. This gives you a better opportunity to increase General fitness.
For either short or long athletes, at least half of your total cycling time should be in TT during the last 8 weeks of training.
David