Why not choose to design for a monitor that will always use the bezels OR for one that doesn't use the functionality at all?
Yes you can absolutely do what was suggested, and if it works for you great! My questions would be....
Where are these buttons going to be? Are they shifted functions? Are they aesthetically unpleasing?
I'm not sure what you mean with the first question. I have a typical 16:9 monitor, but a lot of the bezels in the mame pack try to recreate the original cabinet, so they are still in 4:3, then the actual gameplay is a very small window. Its cool to show the feature but you wouldn't want to play a long time like that.
Basically you'd have this with a game inlay vs the 4:3 regular game.

A lot of the games have specially designed 16:9 bezels that make the most use of the screen, maybe not true to the original but still better than black.

As for the actual physical buttons, I'd be using the pinball flipper buttons on the side of the CP, as they would be unused with anything but Future pinball.