Nobody is going to move a dotfile as a breaking change in any established software

We have oodles of counterexamples to this. GIMP did it, Blender did it, DOSBox did it, Libreoffice did it, Skype did it, Wireshark did it, ad nauseum. It’s not really as big a deal as you make it to be (or a big deal at all). You have a transitional period where you look for config files in both locations, and mark the old location as obsolete.

It doesn’t change the larger point that GNU is way bigger than Linux, though. There are a tonne of things that are larger than Linux, and GNU is one of them.