Did you receive any treatment from the physio? Were xrays taken to confirm a facet issue and rule out any other spinal pathologies?
I can understand avoiding the low bar squats for a specific time period while getting treatment to correct the issue and allowing the area to heal, but not just stopping low bar squats forever due to a facet irritation. It's like telling a person with patellar tendonitis to stop squatting - they don't need to stop squatting forever; just until they can fix the issue and allow the area to heal a bit.
If there was a more significant injury (stenosis, fracture, etc) there may be reasoning behind stopping a specific exercise but not with a facet irritation.