The standard for vertical arcade game cores is to have the flip exactly the same as the original did. Real arcade machines didn't always flip their vertical the same way. Some games did clockwise and some did counterclockwise. As the MiSTer cores are recreating that accuracy, that means some games will be vertical one way or vertical the other way. If the game didn't offer the option, you had to physically flip the monitor. Of course, this was a one and done solution back in the day as a cabinet only had the one game on it. But for modern solutions like MiSTer, it left some games without a way to flip them in DIP switches or other cabinet settings.
Somewhat recently, there has been an effort to add in the additional vertical flip to games that didn't have it. But this is manually done on a core by core basis. If someone hasn't gone back to add it to the core, it doesn't exist. This next bit I'm less sure about so I'll happily be corrected if I'm wrong but the way this is done (to my understanding) is by using the frame buffer to force the screen flip. The benefit is getting the other flip direction but the downside is there is a small additional bit of latency introduced versus the arcade original no buffer needed screen flip. Depending on the person, this may or may not be a suitable solution depending if they just to play the game proper vertically or if they demand the lowest amount of latency possible. As for being addressed in the future, can't really say. Again, these are being manually added by wonderful people with the know how to do so. I would just think of them as bonuses from the community rather than something that is planned to be done.
The best advice I could give is to look at all vertical games and see what options they have then make your actual CRT's rotation match the greatest amount of games that matter to you. And if another game gets the option later, then that's just another wonderful surprise!
