Won’t the timing of each chipset on each board need to be painstakingly individually configured to avoid latency from a “default” profile used in all chips (which inherently vary between every batch)?
No, because PCIe works completely differently from RAM. PCIe is a packet-based protocol that's very latency-tolerant. (Multi-lane PCIe links may require deskew but that's a standard feature that has existed all along.) I think it was Marcan who tunneled PCIe over RS-232 and the chips didn't even notice.