IMHO there is no reason NOT TO do it this way, unless you are in-love with the crappy DVD menus they put on discs (I hate them with a burning, fiery passion in almost every case - they're garish, poorly designed, hard to use, and often poorly performing).
If you want the extras, just rip them to their own MKVs.
MakeMKV is awesome for this task. When/If it ever comes out of beta and actually costs something, I'll be first in-line with my credit card in hand.
You are right, there is no reverse to this. To be clear though, as long as you don't re-encode the videos, you aren't really "transcoding" them. You're just wrapping the existing video streams in a different wrapper. That's different than transcoding which means "converting a video stream from one compression to another compression type" (changing from MPEG-2 to H.264 would be a common use nowadays). Transcoding usually (though not always) means a loss in quality. Remuxing (changing the format on disk) does not.
That is not to say you couldn't re-author a DVD directory structure from a MKV source if you want to (you'd just need a DVD Authoring application that accepts MKVs, or something you can create from the MKVs). It wouldn't "magically" give you all those original menus and whatnot back though. You'd be making a new disc structure from the existing video data. I don't know why you'd want to do this unless you had a friend who you wanted to burn a copy of a movie for their set-top player or something.