I know that under Linux UAE must run as root and have fullscreen support compiled in to run fullscreen in Xwindows.
Personally I don't like my programs running as root - so I upped the resolution to the same as my Xserver - the effect is pretty much the same as full screen.
(I use AmiWm in Xwindows - so it's pretty aesthetic as well).
With SVGA it would (theoreticall) have to run root as well - but I'm having some probs compiling it, so I can't comment on this route.
Cheers.
Siggy.