Well, as you can see you still have all those command line options in there?
mame64.exe flyboy -rompath "C:\MAME\roms;C:\MAME\roms\MAME BIOS" -keyboardprovider dinput -artpath artworkgameex -notriplebuffer -frameskip 0 -syncrefresh -nothrottle -nowaitvsync -video d3d
So nothing has been disabled.