> This repository contains the source of the Tampermonkey extension up to version 2.9. All newer versions are distributed under a proprietary license.

You can of course do whatever GPL allows you to the code in the repository (so up to version 2.9).

so the newer version isn't even at all based on the one before 2.9? seems unlikely

If you own the rights to software, you previously releasing something under the GPL does not mean you have to make derived versions of the thing you released under the GPL available under the GPL too. If you take someone else's code under the terms of the GPL you have to do that, but that does not seem to have happened here.

That assumes that nobody contributed to the software while it was GPL, unless there was an explicit contractual copyright transfer.

It only assumes that there were no copyrightable contributions that weren't replaced as before the license change. Not all code changes meet the criteria for copyright.