Are AT and FTP Detection working correctly with my Athletic Profile?

So, I’m not sure why you are comparing these two workouts…
Santa Rita is an pretty straight forward Anaerobic workout:

While Mono is an Over-Under workout:

As others have said FTP is most ‘accurate’ to prescribe workouts close to FTP. As you get further away from it, it gets less and less accurate. So I would definitely turn off ERG mode of something like Santa Rite and just go by feel (AKA all out). For example, my FTP is 295 and the prescribed target for those middle intervals in Santa Rita is 368W. But if I were to do this workout I would most likely want to be doing that at more like 425-450.

However, because TR has to prescribe some percentage for these workouts they will most likely put down a number that is achievable for a larger number of people at a given FTP as opposed to putting a much higher number for those that have a better anaerobic capacity.

Santa Rita should be working your neuromuscular and anaerobic systems while workouts like mono should feel much more like they are working your cardio.