The license wasn't changed. But yes, generally you can make changes to MIT code that aren't released under the MIT license.
> It's definitely the case that at a given snapshot of the repository which has copyrighted code owned by someone else the copyright notice has to be there at that same revision.
This isn't in the license. Where is this laid out?
MIT license is very permissive but the original author retains copyright and one of the very few restrictions is that you must maintain the original authors copyright notice. So you can use MIT code in a GPL project but you can't remove the original copyright notice and MIT license text.
I don't quite follow your thinking about removing the notice but having it somewhere in history; a given snapshot/ revision will be a distribution where someone can show up and download just the master branch newest state and not the full git history. In which case you surely have distributed a copy of the copyrighted MIT licensed code without complying with the terms of the license, right?
> It's definitely the case that at a given snapshot of the repository which has copyrighted code owned by someone else the copyright notice has to be there at that same revision.
This isn't in the license. Where is this laid out?