Right, it isn't a Nintendo theme issue, it is a game fitting well to the cabinet issue.
If you want SMB on your cabinet, Plan A is to make sacrifices on the controls to water it down for more games, which is gonna kill the DK experience. Plan B is to jump through hoops to make your cabinet transformable in monitor and controls, which I think in this case will still hurt the overall cabinet experience. Even if it doesn't, Flynn's Arcade can already play SMB dangerously well. I don't see the point in troubling yourself with swappable panels over a few horizontal games in this case.
I can't fault you for trying to get some more games out of your cab and ArcadeSD board, so I was recommending some 4 way vertical games that would at least play well on the cab, even if they don't fit in the theme.
By all means, give your panel the molex disconnects, whether you go swappable or not, it is a good feature for a cab. And like you said earlier, a 2nd panel would be a "Phase 2". You can make that decision when you get to that point. I really like this project, and if you can nail that ultimate DK experience, you succeeded. I will be guaranteed to drool in awe of your work. Whether or not it plays any other games is a minor thing in comparison.