The plugin system itself was probably already in the making, and they just chose to implement this tiny feature as a plugin to try it out.
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.
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.