The cam rides in the crankcase, not the cylinder. The lower rocker arms are attached to a pin in the cylinder, so the small change of leaving out the gasket wouldn't have any effect.
Originally Posted by YamaGeek
I have to wonder Dan, does leaving the base gasket off tighten up the mesh between the upper and lower cam-drive gears? I'd hate to think your mod will cause a catastrophic cam gear failure, but that 0.5mm thickness being removed has to make the cam gears mate up much tighter, which can't be a good thing.