>Expected result? (how does a good screen look like?)
No Canon standard firmware bars with the vertical grey lines on the left and right, so a clean and a little bit larger screen of the camera's live view, see this image:

>There's no focus box either; how did you hide it?
The only two settings I made in ML is "Clear Overlays: always" and "Global Draw: off".
"Focus Box Setttings" is set to "Display: Auto-Hide", but I guess this is the default.
>The bars are not symmetrical (both in position
>and colors)
Colors are correct in "real life" - it is justed caused by my bad smartphone camera quality

But you are right that the live view is not centered on the external monitor. But this is only a matter of the external monitor: I had to set the "mirror option" in the external monitor, as a workaround, because the mirror setting in ML does not work for the HDMI out, as you know. If I do not mirror the video signal in the external monitor, it is perfectly centered. So not an issue of the video signal of ML.
>Is the clear overlays feature working properly on the built-in LCD?
Yes, on the build-in LCD it is
always perfectly cleared, on the external only
sometimes when I switch on the camera and
never, when I take a photo (when the live view gets black and switches on again). It is important to know, that I am in the Movie mode of the camera. If I switch to M or another photo mode, the display is cleared well after taking a photo and going back to live view.
>Reproduced the display orientation issue on 60D, but apparently
>this one is handled by the built-in LCD controller, so it's very hard to fix.
That would be bad, because I would have to live with my workaround to set the mirror option in my external monitor which leads to a black stripe on the right, because of it's issues no centering the image when in mirror mode. See also the current picture.
PS: Maybe interesting to know: normally I set the movie resolution to 640 Pixel in the Canon, which can lead to the described bug of the stripes
right and left until pressing the delete button twice.
If I set movie resolution to 1280 or 1920, stripes appear on the
top an bottom, if the bug occurs. But when pressing the Delete-Button twice, the video signal is also scaled, without the stripes (as in the 640 mode).