Unfortunately, it would be a complete guess (I've never worked in recruiting, but perhaps someone reading this can shed some light). From a general military administration perspective however - the more people that need to see a file before action can be taken automatically means it will take longer to process. There are a lot of people in the chain who process these files at varying times. It's a fairly bureaucratic system which (in my opinion) can significantly slow down the process.
Can't speak for everyone, but in my own narrow experience with the Army there is less of a focus on your particulars (gender, race, age etc) then on how good of a soldier you are. If you use "difference" as an excuse for being a poor soldier, you tend to get marked for it. If you are a good soldier, you'll convince a large majority that "difference" really means very little in terms of the respect you get from your peers. Those who would have problems are likely the same kind of people who would be difficult regardless of where they were employed - but the CAF has pretty straightforward guidelines as to how to deal with racism, harassment, etc.
You will run into issues of the system (and instructors, peers, etc) not being sure how to react/interact due to a lack of knowledge and/or experience. Most of these can be cleared up though being straightforward with your expectations to clear up confusion (for example - "I am legally classified as (X), and would be expected to be treated as (X). I'm a recruit and expect to be treated like any other, etc). The system DOES know how to handle recruits - and avoids singling you out for special treatment. Might as well be as upfront with the recruiters as possible - so there is no confusion later on down the road.
As far as the in and out of how your particular transition will impact your application process, medicals, etc - I'll leave that for commentary from more qualified individuals.
