Are you fitting electric or IC? I don't know if those exhausts are practical or not. If they are you may need a gap around it, they can get very hot and paint damage is likely, possibly grp resin burning too.
A hole saw can be used with finesse, but usually only good ones. There's some out there that are split cylinders, fine for plumbing the house but less so for fine work, others are not concentric to the pilot, or even not round. Drill the pilots hole first and then introduce the holesaw gently at high rpm, that prevents the saw smashing into the surface when the pilot goes through, and the speed stops it from grabbing. Chipping will only occur through being clumsy, control the saw and it is fine. If you can come in from both sides then a clean hole will result. Chatter can be avoided by applying a very slight angle. However, in the absence of a range of quality holesaws, or just not having the right size, I find a rough hole enlarged by a sanding drum in a Dremel gives neat controllable results. Filing can force delamination, it's great that it worked for you though. Any method needs caution.