PCIe PRSNT# for bifurcation
The PRSNT# connection is there to tell the host the maximum number of lanes connected, so the BIOS knows which lanes might have link partners and can test for them.
Bifurcation is a different matter. After the host determines the card size with PRSNT#, it will detect the link partners and then continue lane width training within each bifurcated lane set.
So if our card has 16 lanes arranged as 4x4 (e.g.; an NVMe adapter with four M.2s) it should ID on PRSNT# as a 16-lane card. The BIOS will then try to train up and enumerate four endpoints out of those lane sets.
In other words, if you wire the 16-lane card to say via PRSNT# that it has only 8 lanes, BIOS will think it is an 8-lane card and only try to identify link partners on the low 8 lanes.
So your x8/x8 bifurcated card should nevertheless be wired with the PRSNT# pins set for 16 lanes.
Yes, the host could ignore PRSNT# and simply test for all 16 link partners, but that’s not how PCIe is set up to work.