Base gaskets are paper thin... the space you are gaining is fractions of a mm. Ive never heard of replacing the base gasket with gasket maker. However you may be correct. Im pretty sure that when the pistons are made they have accounted for the gasket in the bottom end but i cant tell you for sure. One last thing... if you are already worried about detonation at 10.5:1 compression you may not want to go much higher anyway. Once you reach around 11:1 you almost have mix racegas in with regular and thats without a timing advance.
Not unusual at all, but it does depend on which engine your doing it on, and what configuration your doing. I personally dont know anyone whos done it with the Raptor engine, I'd have to check and measure everying to see what it would gain, and if theres sufficient room for everything to do it. You'd typically use something like YamaBond or HondaBond for a base gasket (and absolutely NEVER for a head gasket), and never generic gasket maker stuff you find at the auto store.
All piston-to-valve clearence (p2v) and compression measurements are based on stack height, which include the head and base gaskets thickness among other factors. They can run anywhere (typically) from .005" to .040". You can call Cometic, and order replacement gaskets in different thicknesses.
For example on my GSX-R, I took .018 off the head, and .004 of the top of the jugs (both to reduce the squish band for better detonation properties). Now this normally would not be a problem with stock pistons, I'd still have sufficient p2v clearance and get a nice little bump in compression. However, I am running Wiseco 13:1 771cc pistons.
With those pistons and stock gaskets, and the milling I did, that would bump the compression up near 14:1 which is too high, and the p2v clearance would be non-existent (theres nothing like a valve hitting a piston, and throwing a rod through the case at 11000rpm
).
The solution is to use a thicker base gasket, in this case .022 over, this way the tighter squish is maintained, and I keep the compression at 13:1. A quick call to Cometic, and viola a replacement base gasket .022+. Best of both worlds.