Hi A1ex, I've uploaded a bunch of files for you at maxotics.com/photos Enter "focusdotshotpixels", then you'll see a link for download
Rewind, if you're interested, you can see the focus pixels in the blown out areas AFTER PDRing in "1280x434_PDRd_HotPixels_BlownOutAreas" I wish you'd go shoot more so you can confirm that this won't be a problem for you (others) down the road. The edge pixels you're seeing, is part of the problem PDR struggles against. There are too many focus pixels for it to deal with without removing more than one would want.
A1ex, you can see hot pixels in the "HotPixelsInRoad" example. (There is a lot of moire with this camera in non-crop mode.)
In the zip, you'll find frames that I shoot in a light table to get focus dots. I then use Photivo (as Rewind helped me with) to isolate the dots through elimination of green channel and other contrast/image type adjustments. I want light pixels on black. I wrote a .NET program that will scan the image and create a dcRAW format hot pixel list. I did one for both red and blue and red only.
In the file "1280x434_PDRd_HotPixels_BlownOutAreas_SeeDeadPixels.jpg" you will see that these hot pixels are actually black pixels from the sensor. My hot pixel locator would have to be adjusted to find those. I can do that later. (This while I'm porting this over to C# and trying to integrate/use g3gg0's code, and C stuff from the libraries---my head is spinning!).
I've been thinking about the median filters a bit too. I think there is an even better application for what you're looking into--reducing moire.
Look at "1280x434_MoirePattern.dng" Seems like a lot of interference patterns that could be predicted/isolated?
It seems to me, much of the moire is because the chroma information for what should be one scan line is split up into 2, so to speak. I understand moire isn't talked about that way. But I believe a median filter on, say a group of 3-7 pixels, with a lower/higher line, slightly offset to right or left, will eliminate the moire, though will blur the image somewhat (which is what a VAF filter would do anyway). Such moire reduction would need a rules-based algo matched to some sort of median filter. Anyway, I may be crazy, but I believe one/we could do through programming what the VAF fitler does physically (better join skipped lines from the sensor).
I understand what you may really want is a RAW frame with some hot pixels mapped to dcRAW. I could shoot something with my 50D (which doesn't have the Hybrid AF dot issue). But I hope you'll segue into our EOS-M nightmare

As you can see, I have some equipment set up for testing. If you need any types of images (you too Rewind), let me know!