I've got a temporary solution to the interface bug that seem to work fine for me. It has to be done every time I launch the game, which is a bit annoying. I don't know why it works. Here are the steps:

1. Have a working mabinogi installation using the bottles method.
2. Start the "Debugger" in the "Legacy Wine Tools"
3. Input "bt all" to start tracking
4. Start the nexon launcher and then mabinogi. Game will likely crash.
5. With the nexon launcher still open, go to "Game Configure", then "Repair Installation"
6. Start the game again. This time the check boxes should be clickable and the dropdowns functional.

One thing that still isn't working is the in-game cash shop interface. But at least I can just purchase from a browser outside of the game.