> specifies all sorts of things about how other things on the motherboard communicate with each other and with the CPU

That used to be true, but I dont know how true it is now.

Once upon a time, ISA and ATA were both wired right to the bus.

By the P3/Athlon era everything was probably on a super-io controller and or south bridge, but that communication towards the northbridge/CPU was over PCI or ever fancier links.

But the clear cutting point to me is EFI. Most of the standards in how things communicate on older PCs was more based on the IBM BIOS. Early clones couldnt exist until that was nailed down. But... EFI replaces all of that with a new abstraction.