Obviously I'm not Canadian, but i know that for some time the UK military have allowed Transpeople to serve and indeed transition whilst in service. One of my very good friends is fully postop and serves on active duty as a pilot in our Airforce who actually even helped pay for her treatement, so that it could be completed quickly and with minimum disruption.
You need to find out before you start, because you cant just stay on T-blockers longterm. The human body needs one or other of the two sex steroids to stay healthy and if you block one then sooner or later (within a couple of years) you have to take the other, and when you do then "developments" will occur which will be impossible to hide in the intimacy of a barracks.
So you will need to be out to your unit by then which means doing your research and asking the questions now, before you sign on. If you do it now then worst that can happen is you have to make a choice between treatment and service. if you leave it, and then they find out that you have been less than honest it could become disciplinary, so hopefully someone can tell you the answer soon.
I think I recall reading that canada is like the UK, in which case you should be fine.