Yeah, licensing is funny. I know a couple who are an RN and an LPN from Ontario and moved to AB. The guy who is an RN got his license right away, just a formality. The woman, the LPN had to gather her documents and present them to the association of LPN's or something and it was basically up to them to say yes or no but they did not give her any problems.
I do not know anything about physiotherapist licensing but here is some info:
http://www.workdestinations.org/view_profile.jsp?occupationUserDatumId=10674&profileUserDatumId=10678&lang=en It has the contact info for the college of physiotherapists and how to get licensed.
As for if somebody can do this on a temporary work permit, the test, I don't see why not. Working as a physiotherapist aid, as long as you get another LMO and a work permit issued for that position, no problem. Courses for people on work permit I believe should be like other courses you don't need a student visa for, that is shorter than 6 months. Call CIC and clarify if you want to be sure. If you want to take a longer course, you would have to apply for a student visa.