What you mean is the processor instruction set, which does affect the physical structure of the processor. You cannot just change the programming/microcode of the processor to have it use a different instruction set.

Because how can linux ARM run on a device that used to run windows x86?

I don't think that's possible. It is possible to have a translation layer, so that individual programs that are compiled for one instruction set (e.g. x86) can be run on a different instruction set (e.g. ARM).

But I can't imagine such a translation layer working for the whole OS, as something still needs to tell the processor how to do the translation. Theoretically, the translation layer could be baked into the processor, but I have not heard of that being a thing, so far.

Is your question inspired by something specific?