No, MKV does not support DVD menu structures. So that's what I meant by "pare" it down. Cut down the frills, like extras and menus.

MKV as a container can hold the movie and its associated playback dependencies/features (multiples of each), such as subtitles, audio streams and chapter marks, even metadata including posters. Video codec support is flexible, so for a fast rip you can stick with MPEG2 which is the native format of the DVD, or you can transcode to something else to save (more) space.

MakeMKV does not transcode the video. You'll be left with a file containing the content you've chosen in its original encoding (video as MPEG2, audio as DTS, AC3, etc..)

MakeMKV can work directly off a disc as it contains its own copy of DeCSS, but I suspect it can also read from an ISO or perhaps a DVD folder structure if you've previously already ripped the disc. I haven't tried it myself, but plan to shortly. Normally I've used DVDShrink to make DVD folders and ISOs - which I've then kept or transcoded with Handbrake to something smaller.