Using a PCI setup is the same as using a CSPPC card, they were not in Amiga's plans and are not "original hardware,"
Not entirely. You can use a PCI sound, video or scsi card with the same software that runs on an a2000 back in the day.
The plan for backward compatibility was to have a new version of AGA render into graphics memory on a PCI graphics card, it would make sense to do that too. That plus a 68k core could fit in an FPGA. If you use one that supported PCI express then it would make a really nice cheap motherboard, it would sell more than an X1000.