I've cut a number of large holes through gelcoat, glass, etc. Other than the size/type/location of hole (e.g. enough working room to accomodate the saw is often the largest obstacle), I prefer a jig-saw. Two considerations for the jig-saw:
(1) Employ the fastest (highest rpm) jig-saw you have or borrow one; and, (2) use only the absolutely smallest toothed jig-saw blade you can accomodate in your jig-saw (something along the lines of a very fine-tooted metal blade). Under no circumstances use a wood (large serrated course-toothed) blade.
Two considerations for the drilling of the hole itself:
(1) Consider the size and the weight of the roof piece which will obviously be falling and separating from the roof. Be careful - you don't want the piece you are removing to rip away from you under its own weight and tear off from the roof (this would be a bad thing). Therefore, consider drilling two pilot holes and making your cut in two, divided into sections, or ensure someone is below to support the piece as you finish the last cut to catch the piece from ripping off and damaging the roof; (2) Take some heavy mil clear plastic and outline your area from under the roof with plasitc secured to the ceiling of the cabin to catch the dust and debris.
You will find by using the finest blade and fastest (highest rpm) jig-saw you can use will leave remarkably very little dust when you're finished. The line will be incredibly tight. The rotozip, well, my experience is you'll be completely covered and it's quite the mess.
m2cw