Don't worry about the current unified behavior. For many cameras, the old value for RAW_PHOTO_EDMAC would often result in image buffers that needed to be skipped ahead by some amount (usually 16 pixels) to have proper alignment. Once the fullres-silent-pics branch is merged, this will no longer be the case on most (or all?) cameras.
Right. Some more background info about this change:
This value for EDMAC is the one used at photo capture step. The previous one was from some other postprocessing stage, and usually different on each camera. From the capture to the CR2 and then to LCD preview, there are a bunch of postprocessing steps, like cropping some borders, FPN correction, bad pixel correction, maybe digital ISO (e.g. on 5D2 at ISO > 1600) and who knows what else.
The fullres silent picture code only calls the photo capture step - but not the processing into CR2, YUV, JPG and so on. So, right now I'm sure I'll get the original RAW buffer, as captured, and the behavior will be consistent on all cameras. Furthermore, since the buffer has the data before any postprocessing, modifying the data in this buffer is very likely to end up in the CR2 and the JPG; before, this happened on some cameras, but not on others.
So, this was a good opportunity to make sure the photo raw behavior is consistent on all cameras.
Bad offsets could cause subtle issues that are unlikely to be reported as bugs, and very hard to track down (ML uses these black borders for noise analysis, so any exposure or postprocessing tool that relies on this would give inaccurate results - from slightly weird to totally broken).
There's still a minor issue with this approach: the DNG might be a few pixels larger than the CR2, so the skip offsets might not match. This will only be an issue if you will take a dark frame from a few hundreds of silent pictures, then find out it's not perfectly aligned with your CR2's. Should be easy to fix in post though, and those shooting astro certainly have the skills to do this.