Yes, yuy2 and autoframeskip are given as parameters in the sdlmame-start.sh script that the desktop file points to.

It must have been late when i put together that last upload. For the next upload i have migrated all the command-line parameters from the startup script to mame.ini and the startup script just specifies the inipath (/home/user/.sdlmame). I won't leave a backup copy of mame.ini in the /opt/sdlmame directory, just install it in the user config directory if it doesn't exist.

The 'q' key ('1' in Fn-land) is both the player 1 coin and player 1 start key. This seems to work ok in the games i've tried--you just press it twice to get going.