I already posted about my carbon fiber helicopter boom, for that I decided I'll bite the bullet and do alloy molds. 
I also need a carbon fiber helicopter canopy. Similar shape to a football but a bit bigger and open at the back, I'll attach a pic of one. It will have pretty thin wall thickness, generally they are about a half mm, maybe .6 or .7. So only a couple layers of weave. 
I will be making my own design on fusion 360 and milling the plug on my cnc. The process that makes the most sense to me is milling each plug half (mold will be split down the middle lengthwise, right and left half) out of mdf or foam, spraying it with layers of duratec primer, sand and polish, then attach each plug half to a flat sheet of melamine or some other rigid plastic to create base for mold flanges and proceed to make fiberglass mold halves from that. I would prefer to skip the plug stage and go straight to milling the molds, but it just doesn't seem to work out as well as making fiberglass molds from a plug.  From the female molds I will vacuum bag a carbon fiber wet lay up. 
does this sound like a good plan or is there an easier/better way considering I have a cnc? Another variation would be attaching the 2 plug halves together to make a complete plug before applying duratec,  then split into 2 molds using the method shown in the air box video, but i feel that it will be less work to just attach the 2 halves to flat sheets for making the molds, just need to make sure both sheets are perfectly flat planes. 

Depends on if you're using a brush or spray viscosity tooling gelcoat. If you're using Unimould then its brush viscosity and it wont spray through a regular gun with a 2.5mm tip, you'd need a 5 or 6mm tip on a gelcoat cup gun.

But yeh as you said, it doesnt matter. The only benefit to spraying over brushing is application speed, so it's great for big parts that will take a long time to brush up because you can spray it in 5 minutes. It's also slightly easier to get a consistent thickness, but if you've got a brush viscosity gelcoat then that shouldn't be a concern either. In any case, you shouldn't need to spray it for these pieces, it'll take 5 minutes to brush on.