Pin-mapping (non)conventions for custom Arduino boards?

maintain my own forks of various libraries with the pin numbers changed / settable in constructor.

Yeah, I feel your pain. IMO, all pin assignments should be given in the constructor. The biggest annoyance here to me is libraries hard-coding their SPI chip select pin. I find myself refactoring libraries all the time to account for this. Not sure if it's too late for this, but I would really advocate for Arduino to pick up that standard.