Next release (hopefully) will implement a somewhat smoother mode switching (you shouldn't see the desktop flashing on the background anymore). So performance on mode switching systems should improve.
With regards to using RGB for old composite video systems, the thing is you can emulate composite through an RGB output. MAME already has a NTSC filter, although I haven't had the time to test it seriously. This would allow emulating the Sonic waterfall effect, for instance, or the artifact colors of King Quest.
Yes Calamity (and the rest), using direct RGB output can "distort" the "real" emulation, mostly in those games/consoles that took advantage of "analogic processing" for visual effects. Of course there is a lot of examples where developers "squeezed" the hardware achieving really cool effects back those days, but for most of the games, you get better a better look and of course you always can use .ini files for those "special" games.
Keep in mind that display memory buffers are (were) natively progressive. Interlaced display was invented at the same time than television was, because it was impossible to scan a TRC fast enough 60 or 50 times per second, using vacuum tubes back that time. So camera and tv sets, both scanned in an interlaced way (actually interlaced scan is a way of "analogic" compression...funny uh?).
When "television" had to display electronic generated images, things got complicated because of interlaced scan...ringing, aliasing, combing...a lot of undesirable effect appeared.
Fortunately, arcade industry did not have to stick to NTSC standard....but home consoles had, and sometimes they used it in their own benefit.