Right, what @bouncyball said.
For an illustration of this,
check out this post from a while back. Thought I found the Holy Grail but it turned out that the cure turned to be worse than the disease. (I sometimes throw around these technical terms when communicating with developers.) Ok, kidding aside there might a video stream that doesn't show these focus pixels but we haven't found it yet.
I took another look at the @martinhering focus pixel files and I'm still scratching my head at how these work because some of the maps have pixels next to each other on the horizontal axis, others are missing sections and still others have focus pixels mapped in areas that we know there can't be any focus pixels because that it is an inactive area of the raw buffer. There are also some video modes that are missing, like zoom mode which has a full raw buffer size of 2592x1108 and can move around the sensor like this:

That caused all sorts of issues when I tried coming up with a focus pixel map file that would take care of all possible raw buffer locations. I ended up just stacking all 21 raw buffers in Photoshop. This might be overkill because if the raw buffer happens to be at the top or bottom of the sensor it might be in an area that doesn't have any focus pixels but since we don't know the position of the raw buffer on the sensor we need to account for all possible locations.
Another challenge is with the crop_rec module. On the EOSM (and my experimental version for the 700D) it uses the mv720 full raw buffer (1808x727) with a 3x3 pixel skipping pattern and the focus pixels that show up on both the mv720 and mv1080 video modes appear on the image. I thought that using a combo map would work for both the crop_rec and mv720 video modes but after extensive testing with Danne, we found out that it doesn't work that way and we always ended up with at least some focus pixels showing up on crop_rec footage like in this example:

Adding some Chroma Smoothing helps get rid of these in raw video but crop_rec H.264 footage also shows focus pixels and removing these in post production is even more challenging.
I have yet to test the 650D and 700D though.
I've got a 700D and can provide you with test footage for all the video modes. I believe I read somewhere that you needed a blank wall at a certain exposure, could you please post exactly how you would like the tests shot?