There is no standard for SoCs. If your board has an NXP i.MX6, you can't just desolder it and drop in a TI Sitara or nVidia Jetson.

Designing a PCB for an SoC isn't rocket science. There's nothing magical about the schematic or the layout, and usually the vendor gives out full design files for their eval boards that you can use as a starting point for your product. The silicon is the hard part. You can make your own Beaglebone clone right now for a few hundred dollars including parts and the board, assuming you are comfortable soldering smt. Making a fully open equivalent to the Beaglebone SoC is a nine figure endeavor at a minimum.

The reason you don't see hobbyist x86 SBCs is that Intel and AMD make customers sign a large pile of NDAs before sharing the documents you'd need to make your own. And in the case of Intel, you need to pay a 3rd party to provide you with a BIOS framework that obfuscates the ME firmware and other blobs (like memory training) so that even the board manufacturer doesn't have any idea what's going on in those hidden processors. (source: used to help develop x86 server hardware)