The process is still the same, even if you're a Canadian student. You'll have to send in your high school transcripts and IBCC will deduct ten percent from your score. We're not sure how the conversion process actually works.
You'll apply through the Pakistani embassy in Canada. They'll send your application to the Higher Education Committee in Pakistan. The embassy is also where you can get the application from. You should start the application process at least six months in advance.
There will always be jobs for doctors, whether in Pakistan or in Canada or the US or anywhere else. A lot of people end up staying in Pakistan simply because they don't take the board exams, they do poorly on them, or they can't get a residency.
Having done a physiotherapy course won't change the admission requirements for you if you want to do MBBS. The two are unrelated and credits don't transfer. It also won't matter where you've done it from, you'll still need to apply to the MBBS program the same way as everyone else does in Pakistan.