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.
Note, however, that there's a lot of "quirks" and similar device-specific corrections for x86 as well. These get presented to Microsoft by the manufacturer, and Linux gets to reverse-engineer them.
I was aware of being able to have ex. u-boot pass a device tree file to the kernel at boot time; are you talking about that, or something more generic?