I would listen to the bike fitter.

did the PT actually LOOK at how you ride? Figure out what muscles fire at what time during the revolution? Hook you up to a biofeedback machine to monitor co-contractions of the hams and quads?

(knee issue folks in particular will need co-contractions so the hams can stabilize the knee joint itself during the quad contraction as you push the pedal down, unless you have massive hams that can do it just by bulk. we've had patients who did exactly that. overdeveloped hams can only help someone with ACL/PCL/LCL/MCL issues, never hinder) (mind you, that's overdeveloped, not overtight. gotta stretch and strengthen)