and/or maintain my own forks of various libraries with the pin numbers changed / settable in constructor.
That might be a bugger to maintain, although if it's just a few tables you could diff the files when there's a new official release, one wouldn't expect too many changes until a new board comes out.
"Arduino Pin Number" vs. port/bit seem to be in no particular order.
I noticed that on a Mega clone I'm designing, I've done my own (much more logical :)) pinout, but then my board is not physically compatible so it's less important.
Rob