Ryan, there are many different ways to accomplish the same thing. The only thing I can tell you is if the roof wasn't built to hold the weight
, don't put a roof A/C up.. or you're liable to end up with a big skylight when the A/C hits the floor.
Losing a window is a concern. But, remember... you only need to have a window A/C when needed and they're cheap to replace (in the grand scheme of things). The other times you can leave it at home. Which is a plus. You can put it in the bottom of a closet, cut a hole through the hull in the front or rear... if that's your need. It's more about what you want to do. Stand alone portable A/Cs don't really work.... if that's what you're asking.