I haven't measured this yet, but I question whether SMT would actually introduce any meaningful jitter into the timing loop. If my event is off by 10-100 nanoseconds, I probably don't care that much.
I am not actually sure how precise this approach could be in theory, so if the noise floor could be low enough for it to matter, then it's certainly a factor for some applications.
If we prove that SMT has a certain bounded impact, then it may be possible to say that for a certain range of applications you get a 2x feasibility bump because you can leave SMT enabled.