GM picks the closest appropriate mode from what's available on your computer. In your setup's case for MK, that is 400x256. As 256 is the nearest multiple of 8 to 254, I doubt there'd be any real difference even if you were able to create a 400x254 mode. The game will still be pixel-perfect, but you'll get an invisible blank line at top and at bottom of screen. I doubt you will notice, especially if you adjust vertical size.
Original arcade games were ONE game per cab, in most cases. So, the operators would put in a game PCB and adjust the screen size to suit that specific game. That's what the monitor's geometry controls are for. If running mame/groovymame, you should not expect every game to fill the screen perfectly, every time you start a fresh new game. Even if you get the video mode and refresh rates etc "just right".
If you have some sound stuttering there's likely something in your audio or video setup making it happen. It might even be something you've changed from default in your mame.ini like triple buffer; syncrefresh; or portaudio. That list is not exhaustive, just what came off the top of my head. The best way to be sure it is "clean" is to delete your mame.ini, generate a new one (mame -cc), then go into VMmaker, click "edit settings", go to tab 4 and make sure you have the export settings box ticked, then click "OK". VMmaker will then update your mame.ini with the CRT settings automatically.