Canon 6D

[Levas]

I’m not very familiar with that function, never use it. But I expect that it alters the sensor read out timing registers (A and B timers)  And if that’s the case, it doesn’t work in combination with crop_rec module, because those registers are fixed in the presets.
Will take a look at it.

[mineralof]

Still, could be a good preset, no stretching in post, 16:9 aspect ratio, but 'just' 40fps.

if possible without skipping lines, this will be an interesting and very high-quality video

[Levas]

BTW is there chance to change exposure in crop_rec mode 50fps? In Image fine-tuning > Shutter fine-tuning. I cannot set 1/96 for 48 fps or 1/100 for 50fps.

Image fine-tuning > Shutter fine-tuning won't work when crop_rec module preset is used.
Both make use of overriding A and B timer registers, where crop_rec module preset seems to be the one overruling the other.

But tested with the latest uploaded build, I can get the following shutter times in 50fps preset.
With shutter value set to 'original' (option in crop_rec submenu, q button when you're in crop_rec menu) I can get these values:
1/64 - 1/84 - 1/100
With shutter value set to 'full range' I can get these shutter values.
1/50 - 1/65 - 1/78 - 1/100

Are you sure, you can't get 1/100th ?

Oh wait, to my amazemend, I see the FPS override option does really override FPS, even when crop_rec module preset is used.
There I couldn't get 1/48 or 1/96 shutter speed when overriding to 48fps.
But it's not a good idea to use FPS override in combination with crop_rec module, probably works for slowing down (from 50 to lower fps).
I expect no problems when lowering fps, but I'm not 100% sure though 
I expect overriding it to faster fps, will result in corrupted frames, because most presets have very little headroom for highering fps/resolution.

[Levas]

if possible without skipping lines, this will be an interesting and very high-quality video

There will still be skipping lines, but the mode is the same as normal 1824x1026 raw recording. (3x3 (horizontal binning, vertical lineskipping, no stretching needed)
For absolutely no lineskipping and pixelbinning, you should try the 48fps preset that is in the 1:1 pixel readout crop preset.
There is a preset in there 1840x908 @ 48 fps (no need to switch camera to 720p mode) only caveat, crop factor is about 3x.
So your 35 mm lens will become about 100 mm 

I'm working at a new structure for high fps modes.
The same like I did for 1:1 and 3:1 readout presets.
I want to have all fast fps under one preset, with resolution and fps options in a submenu.
This way I could easily add more fast fps presets, like 48/50/60 fps options and also max resolution in 40fps etc.