Given that .MP4 is now the only format for eztv and other sites your wish isn't going to come true. Occassionally you'll get mkvs if you look hard for shows (normally full seasons at a time) but mostly mp4 now especially if you're using an RSS feed.
Thus since I want all of these to show up in Recorded TV the only solution is to convert them to WTV. Unfortunately I have yet to find a good process. The process should be the same for .MP4 AND mkv, just have to nail it down.