I just spent several days testing full-res silent pictures functionality.
I used ML nightly build for 5d3 from April 28, 2015.
I tested silent pictures with 2 lenses: EF 24mm f/2.8 IS USM and EF 100mm f/2.0 USM.
Setting aperture does not work on 24mm lens. The photo is always taken on the widest aperture which is f/2.8 for this lens.
Here are 2 images.

Left one is a master CR2 image taken with all ML settings off. I had to put markers indicating distance from tripod in my backyard

The camera was focused on the nearest marker '.8'. Aperture set to f/22. You see that all the markers are in focus.
Right image is MLV image taken with 'silent.mo' and 'mlv_rec.mo' modules. Silent picture settings were set to 'full-res'. Exposure simulation and exposure override were enabled in ML menu.
Camera was focused on the same point.
However, the picture was taken at f/2.8.
At the same time setting aperture works with EF 100mm f/2.0 USM on the same camera with same ML build.
Summary:
1. Liveview says that picture will be taken at f/22.
2. Exif says that picture was taken at f/22.
3. Actual picture was taken at widest open aperture.
4. Setting aperture does not work on EF 24mm f/2.8 IS USM and works on EF 100mm f/2.0 USM.
Sounds like expo override may not work with STM lenses. Any other STM lens users can confirm?
EF 24mm f/2.8 IS USM is not STM lens, but aperture does not work on it too.