I'm very dubious of your plan to manage copyright at the level of commits - i.e. one copyright and license up to a particular commit, and another for subsequent commits. This is very unconventional and sounds like a recipe for legal confusion. You can't meaningfully pick apart the commits to a single file. Don't try to do this without advice from a lawyer.
I thought it was proper to indicate where the code starts to diverge, by hash. There is no clearer way to designate a point in the development time line where all code is ATI's property before and anything after is a mix and match. I've removed it from the license.
I don't think it's bad to indicate where they diverge (but it would be more readable to reference the commit by tag, now you've imported them).
My main concern (sorry if I didn't read it carefully enough and misunderstood) was that your original approach seemed to me to be saying that there would be files in your distro that had portions under one license but subsequent changes under another. I think attempting to apply licenses to an individual file at the commit level is problematic - hence my advice to just accept that modified files are derivative works and will have to be licensed in their entirety under the GNU Affero GPL.
It's late now, I'll try and review your updates soon.
EDIT: Or put another way - where the development diverges is useful and interesting information, and there's no reason not to include that information. But I wouldn't personally word the license in such a way that it depends on this; such commentary should be purely informational and clearly not part of the license terms.