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I can't answer all of these but I can give you a start.

I don't think anyone knows if 10-bit h264 is even possible, or anything above 1080.  I suspect not, very sure it's not possible currently.
Binning is done at hardware level by Canon.  It collects light from multiple sensels but sends back one measurement, allowing collecting light from a larger portion of the sensor for a lower bandwidth, at the cost of spatial resolution.  I don't know how the sensel data is combined, some kind of average I assume but I don't know which one would make the most sense.  Geometric mean possibly? 
If it's clipped, it's clipped.  Different programs will use different algorithms to try and make the clipping look nicer, but the information is just as lost.  You can losslessly convert mlv to dng and compare recovery in two tools.  I haven't used MLV App, this question is probably better asked in an MLV App thread, maybe here: https://www.magiclantern.fm/forum/index.php?topic=20025.msg243653;topicseen#msg243653

You might get better feedback about the video if you ask here (and explain you want review / feedback): https://www.magiclantern.fm/forum/index.php?board=19.0

Thanks! I will be checking out those forums to see what more I can find. I appreciate you taking the time.

In the meantime, I did a little messing around with various settings outside in the parking lot of my studio. I shot the same shots in various formats including the 6D's own h264 format for comparison. Everything is shot on my Contax Zeiss 28mm at about f/6.3 with a VND filter at 1/50 shutter. All 24fps. All 100 ISO. Nothing was changed (not even focus) and everything was shot in the span of 10 minutes. RAW shots were processed to ProRes 4444 in MLV App with ARRI LogC and then the LogC to 709 LUT was added in Premiere.

4K 1:3 Crop video: https://www.dropbox.com/s/is50a52h4r13nk7/6D%2028mm%204k%201x3.mp4?dl=0
1080 various formats compared video: https://www.dropbox.com/s/idiht9wwwk6ur44/6D%2028mm%201080%20various.mp4?dl=0

Initial findings (I would love anyone's feedback to see if I'm missing something):

1. Raw mode without crop mode enabled is far superior to the Canon h264 (not surprising). Rolling shutter is about equal in both modes and very usable and maybe a little less noticeable in h264. Moire and aliasing is horrendous in both but worse in h264. The power lines and card edges render poorly. The patterns from the shop roll up doors is all over the place. Again, all worse in h264. I wish I would've used a flatter profile in h264
2. 1:1 crop mode is the cleanest but the crop factor makes even my 28mm telephoto. that said, there's practically no moire or aliasing. very clean lines even on power lines. At 100 ISO, the noise in the image is negligible but I would be curious to see how the noise patterns did in the dark at higher ISOs as compared to a mode where more of the sensor is utilized. Rolling shutter is insanely prevalent.
3. 1:3 crop is surprisingly good image wise. If you look at my reference videos, the power lines render really well even when magnified to 100% in the 1080 video I exported. You can see some softness in how the power pole is rendered as compared to the 1:1 cropbut this is surprising good!! The results are astonishing. That said, rolling shutter is increased intensely. Is this due to slower sensor readout or because we're actually recording less horizontal pixels?

I have the Sandisk Extreme Pro 170MB/s card and my SD overclocked at 192 but I can only get about 23 seconds of recording time on 1x3 crop mode. Does anyone have a solution to this?

btw, wanted to upload a couple minutes of test footage I shot yesterday throughout the day.
https://www.dropbox.com/s/n03v5mj8p4mceok/MLTEST1.mp4?dl=0

Focused primarily on getting exposure right to look at the colors/skintones/etc. My post processing for all of these shots was as follows: loaded in MLV app and disabled "Enable RAW correction" because I initially tried a few of those things and got some weird results so I figured I should start with the basics. I went through and maybe just increased/decreased exposure a tiny bit, made slight white balance adjustments, converted each shot into ARRI LogC, and for some shots I checked the highlight reconstruction box although I'm not seeing a whole lot of difference one way or the other. On the last shot of the Old Fashioned, I played with the Chromatic Aberration dials to reduce it a bit. Worked pretty well. I notice a lot of CA on the second close up of my dog at 1:03. I didn't adjust it at on that shot. I think I also started those two close ups on the zoom feature. Didn't realize it would shoot like that. Happy accident?

After exporting in ProRes 4444, I brought everything into Premiere, I simply added the built in ARRI LogC to REC 709 LUT. Earlier on a played with a couple shots which were exported on standard from MLV and found that I preferred the ARRI conversion especially on skintones and highlight retention. I added some warp stabilization to a few shots where it didn't look crazy. I shot this all on a 50mm Contax Zeiss f/1.4 at various apertures. The CA is pretty bad up until f/2.8 so I generally didn't drop below that but if I'm honest there probably are a few shots where I did.

Overall, I'm very happy with the color rendition. I tried to use the histogram, despite it being slow, and ETTR when applicable. It's much better color than I remember shooting in h264 on it back in the day. Being able to adjust white balance in post like I do with RED footage is really nice.

Now my gripes. The first shot, I'm seeing a lot of weird color noise in my dog's coat in the highlights. It also appears on the sunny parts of the fence boards around 1:36. I'm surprised at how well it handled the rug pattern around 0:12. The highlight retention is pretty good. Look at the sky around 1:22. Do you guys think the CA at 1:03 is from my lens or from the crop mode I was in?

Any input would be appreciated.

Levas et al, thank you so much for the work you've done. I used to us ML back in the day when I first started filmmaking on my 550D. I've switched to RED over the years but I've had an old 6D lying around for years that I used to use for BTS until the card slot stopped working. Turns out, using a dud SD card and spraying WD40 on the leads and inserting/ejecting like 10-15x cleans those leads enough to work.

All that to say, I've loaded your version of ML. I've dug through and read this entire thread. I've enabled SD overclocking which doesn't work for me at the highest setting even though I have the same Sandisk Extreme Pro 170 MB/s card you're using. I'll be testing it for fun with my Contax Zeiss Cinemod primes over the next few days/weeks.

I'm wondering four main things:

1) Is there a way to shoot 4K in something like 10-bit h264 without the 3x1 pixel binning? (I have a feeling I know the answer is no)

2) Related to #1, How does the 3x1 pixel binning work and how do I configure it? Moreover, if I'm understanding how it works correctly, it's taking 3 adjacent pixels and somehow averaging the color. When brought into MLV App for post production, does this do very well on parts of the frame where simple color gradations occur and perform horribly in the high contrast areas? Maybe this is better explained in one of the other ML forums. If so could you point me there so you don't have to waste your time regurgitating something that I have to imagine has been asked many times before.

3) I'm having a little trouble understanding exactly how to use the crop modes and how to correctly configure my settings to work well. Is there also some diagram that shows the crop factor in the respective modes?

4) Perhaps this is just my lack of experience with MLV App, but I'm noticing that I'm not able to get the sort of highlight retention through it as I would through taking a canon raw file into Lightroom. Maybe I'm doing something wrong or just actually totally clipping? Admittedly it's been some time since I've used my Canon so I could just be misjudging things slightly. Moreover, is there some best practices for the 6D in MLV App for various modes?

Thank you so much in advance.