It's a little different in this case.
It certainly is. I got a chance to do some quick tests. Please check that I'm doing this right because there aren't really any instructions for this yet.
Let's start with the Canon menu. Make sure to have the camera in movie recording mode. We're going for mv1080 video (3x3 line skipping) so the camera should be set up for 1920x1080 24fps.

Everything else is set up via the Magic Lantern menu starting with making sure both the crop_rec and mlv_rec modules are loaded.

Turn on the crop_rec module and pick the
3x3 720p (1x wide) option. Yeah, it is confusing because the Canon menu is set to 1080p and the crop_mode is set to 720p but it will all make sense in a few steps.

The frame size that I really wanted is 1280x720, that's a 16:9 aspect ratio but the maximum vertical resolution is 692 which corresponds to a 1.85:1 aspect ratio. Ok, close enough and it is a standard cinema aspect ratio so I'm good with that.

When you go to LiveView everything looks "normal" if you've ever shot raw video except maybe the crop doesn't look quite right and there's a little warning sign at the bottom of the screen. If you look back a couple of screenshots you'll see a message saying, "After leaving ML menu, press PLAY twice to enable crop mode."

This is what it looks like after pressing PLAY twice. Wow, that's quite a stretch!

The default settings are for most of the screen overlays to disappear when recording. I find that the best way to frame your shot is to make some marks right on the screen with tape or a marker. Lo-tech but it works.

I haven't shot any video's worth sharing using this module yet but here's a frame of a quick shot using the above settings. The actual frame size is 1280x692 and the EOSM seems to have no problem recording continuously at this setting. That wild moiré going on in the background is due to a window screen. This is "normal" with raw video and these ML enabled Canon cameras (with the notable exception of the 5D3).

So why 720 (or actually 692) and not 1080 and isn't this supposed to be mv1080? The frame full buffer when recording 1080p video on the EOSM is 1808x1190. The camera is skipping every 3rd pixel horizontally and vertically and the maximum resolution of the sensor is 5184 x 3456, give or take. In mv720 mode it is a 3x5 pattern skipping 3 pixels horizontally and 5 pixels vertically with a buffer size of 1808x727. When recording H.254 the frame is scaled up in 1080p mode and in 720p mode it is scaled down but only in the horizontal axis. Ok so in mv1080 mode the ML menu should go up to 1728x1158 on the EOSM like it does on it's big cousin, the 700D (the full buffer is cropped when recording video). However, there's no way to record that much data with the camera's hardware so we're limited to a frame size of about 1280x720. You can vary the dimensions somewhat, it is the size of the frame in MB that matters. Make sense? Good, now can someone explain it to me because I'm not sure I got this right. As far as I know this isn't really documented all in one place.
Long story longer, @rbrune has figured out a way to get mv1080 raw video out of the EOSM. What I'm finding very intriguing is that there are no focus pixels showing up on the frames. Just to make sure I'm not seeing things I used mlv_dump to create the DNG frames because MLVFS automatically masks out the focus pixels. Now how did that happen? Maybe there is an answer to
dealing with focus pixels in camera?