Why do you need to add to your range by putting your ankle in a poor position?
It may not be a loaded position, but reinforcing bad mechanics isn’t good either.
Your body can buffer any deviation in technique for a time until it can’t any more. No warning your done game over.
Here are some episodes that address it:
Pro Episode # 38 – MWod Pro-User Request Friday: Femurs Straight, But Feet Ducked? The MWOD Approach
Squat Quick Test: Is it your Ankles or Hips?
Episode 343: Stop Walking Like the Duck You Aren’t

You are aware of the compromises in position you are making so now you need to address them.
Impacts up/down stream of the  deviation in position will be a problem down the road if not addressed.
Have you mentioned what you have noticed to the PTs?

Have you started looking up/down sream of where you are seeing the issue?
For running instruction go to the Helming Athletics site or on the Cody App. if you have an Iphone.

Yes, you want to keep your big toe on the ground when squatting.
Have you addressed your feet at all?
Pro Episode # 59 – Reclaiming those Gnarly Feet
Episode 337: Long Ruck Feet Or Ultra Marathon Feet?
Ankle rom?
Are you missing rom at the knee?
Community MWod Video: The Knees-In Squat
Pro Episode # 39 – Voodoo Floss Primer: The Knee
Pro Episode # 35 – MWod Pro-User Request Friday: The IT Band Primer
Pro Episode #5 – Knee Stability and Laxity

If something is restricted  you need to address it. There may be several impacting factors.