"there does not appear to be an obvious transposition of wiring"
There doesn't have to be. Looks from the service manual that the encoder has a wiring harness ... it would be possible that the "wrong" part would just plug and play... backwards.
I don't know if sending to Yaesu for repair would be the most cost effective if all that needs to be done is that the encoder pins need to be flipped... because encoders are often kind of expensive and I'd guess the "modification" to just re-do the wiring is not something Yaesu would probably be willing to do.
But you never know, might be worth looking into.
As far as I can tell, the RES20d50-201-1g is what you have, based on the service manual: http://www.nidec-copal-electronics.co.kr/upload/rec_res_en.pdf
They do NOT seem to offer two reversed parts, so I don't know what's up with that.
Any decent tech with a scope should be able to do the mod quite quickly even if it's not obvious what the encoder's "A" and "B" outputs are. Of course, whoever fixed the thing shouldn't have got the encoder swapped anyway.
If it were my rig, I would have just finished cutting , swapping, soldering, and heat-shrinking the green and white wires :-) (Seriously, are they red, black, green and white and come directly out of the encoder? That would be my guess from the service manual's suggestion of part numbers)
You can actually probably check it with a multimeter. One wire (red, if it's the encoder from Copal) should be +5V, one (black) should be ground. The other two should either be 0 or 5, and since they'll change FAST when you rotate the knob, you could check them on the AC meter setting. They should read 0 VAC when you're not spinning the knob and I suppose something in the ballpark of 2.5VAC when you spin the knob... all this should be plugged into J4004 on the panel unit board. There are some test points there, TP4008 and TP4010 should be the "A" and "B"
Anyway, I don't want to give you over-confidence that I'm exactly right about the problem or the solution. I'm making this up as I go along. I just want you to have this in mind when you are looking for repair folks. I don't want you to have to pay for a new encoder if you've got a working one that just needs its leads swapped.
The only tricky/dangerous/risky part of playing around with it is static electricity. The encoder goes straight into an important CPU.
I also don't know exactly what would happen if one of the A or B outputs on the encoder failed in this radio. I would think tuning would be strange and erratic or not work at all, not just smoothly backwards, but who knows...