I am currently running an experiment to kind of answer this exact question! I have a 70.3 as my A race, so naturally Plan Builder put together a multisport training plan. I am ignoring the prescriptions for running and swimming, and mostly just doing both in Z2 (I do the form drills in the swim workouts as well, but that doesn’t really change the intensity I’m swimming at).
I think there are two notable differences in the plans that make the Half plan better, but only marginally so: the bike workouts assume the additional stress of running and swimming like you note, but they also focus on practicing that 70.3 bike leg intensity / duration, which will be a bit different from the intensity / duration of a 40k TT.
With Adaptive Training, I would expect over time that you’d hit the right amount of stress based on how well you are recovering / adapting with the added stress of running and swimming, or the fact that you require less recovery from the easier running / swimming. However, Adaptive Training won’t adapt the specific targeted intensity / duration from 40k TT to half bike leg. At the same time, I feel like that the specificity of that difference is a marginal improvement vs. overall fitness, so if you feel like your FTP isn’t improving the way you want, maybe it’s better for you to focus on just that - and mix in some long rides in aero on your own.