Well, video quality would be the same since you’re not reencoding, and assuming you already have the MKV itself, it would be significantly faster to download. You’d just lose out on the extra stuff included in the BD50 version.
Of course, you’d have to make sure you remux the MKV to include the same audio and sub tracks that are on the BD25 version before you patch it in, otherwise you’ll probably run over on file size and the menus won’t point to the same tracks.