As for the only difference being the file name, that's an untested assumption. Up until now, Claude hadn't supported AGENTS.md, and it's a simple application of Hyrum's Law that somebody, somewhere, was taking advantage of that to give one set of instructions to Claude, and a different set of instructions to some other provider. The correct behaviour in the presence of both files is not obvious, either.
Having a kill switch for the change is a perfectly reasonable safety measure in case something goes horribly wrong.