@drdave79 saving the game option file should work.

Retroarch main menu-> Quick menu-> options-> create game options file

You may have to start a different rom after and change the default setting back though.

So start rom, change setting, save game option file, close Retroarch. Next, play regular game, change setting back, then just exit Retroarch.

Or....

You can also save the game option file then just manually edit the cfgs over network. The default core options are saved to Configs-> all-> retroarch-core-options.cfg

Then just edit the opt file you created Configs-> all-> retroarch-> config -> mame2003 directory-> game.opt

@jrpohlman39 good news... I had the exact same problem a while ago with Robotron. Please see the discussion here:
You can map this in mame menu. Within the game it can be accessed via keyboard by pressing TAB key. You can map player 2 joystick to player 1 inputs.

Even better: with the new and very cool mame2003-plus-libretro emulator there is a core option implemented for this. Once set, it enables this control scheme for all dual joystick games. See this github issue 278 and github issue 216

There is a dedicated thread in this forum for mame2003-plus here