I've never tried any linux build of mame. Are there any benefits of the linux build in terms of input and audio latency?
I will try to answer some of your questions.
audio latency: Linux uses the ALSA architecture for audio output which is almost RT and the audio_latency setting can be set to 1.0 in mame.ini. You have also JACK audio which is RT compliant. But this is not needed to my opinion.
video output: With the proper 15kHz patch, the Linux kernel offers full flexibility in setting any modeline/refresh rate. The kernel handle all ATI driver calls identically for all the card models that support low dot clock. Linux was supporting 6xxx before Windows due to the unicity of the radeon driver.
input lag: Here the situation has never been totally clarified. With devices operating at 1000Hz we can consider that key/joy inputs are processed fast enough to be handled within a unique frame. SDL with open GL is giving the best compromise and mame is build upon this library. Nevertheless, Linux is considered to be alway 2-3 frames behind Windows and is not taking advantage of DirextX related optimisations.
With the recent introduction of the BGFX rendered within mame mainline, mame will be totally agnostic to the way the video is rendered. This allow at the same time some nice shader effects to be introduced within the video processing pipeline (CRT bloom + raster rendering). This could be the next turn in the way switchres will be implemented. I am personally hoping to see the benefits share between both worlds.