Is that shorted the 16x slot with the card in directly or with all cards in via a 1x riser?
No that's the 16 slot shorted exactly the same way as I would with the 1x slots. Short the socket and then plug in the riser.
Do I need to short pin A1 and pin B81 instead on a 16 times slot?
No, it should be shorted exactly as the 1x bridge. PCI-e is a bus, so the slots are actually interconnected on the same lane. I got mine working with 4GPU's that way, never tried 5.