Actually, the physical processor does have, to this day, DOS compatibility in microcode and bios. (Maybe in stub form, running DOS probably won’t actually work anymore with new hardware anyway, I don’t know if anyone’s even tried it in years.) When they say x86 ISA is ‘legacy baggage’ they don’t just mean the silly register layout and instruction set.
The northbridge or HT bridge controls all access to memory, both DRAM and PCI chips (and bios and other device junk), and it’s the one that initializes PCI devices into certain slots. That’s why the cpu, and thus the OS, is incapable of seeing through it.