If this current generation of Hz x99 follows on the design of the original and hence is very similar Jingsha/SZMZT x99.
You had 3 physical x16 but only the top two were x16/x16. the bottom one was x16/x8 (total of 40) and if you popp'ed the M.2 pcie nvme then it robbed an x4 from the bottom x16/x8 making it an x16/x4.
I'm wondering on this current gen how they mapped the second M.2 - if they were lazy they may have robbed from the slot making it an x16/x0 if you pop both M.2's.
Did they rob another x16 slot for the wifi m.2 or is that coming from the legacy x4 2.0 (assuming the x1's also come from the legacy x4)?
I like your idea of PLX the lanes bifurcating the true x16's or at least one of them (I'd actually love to have an extra x8 and give that up from my slot that has my GPU). I too would love to see dual 10gbe sfp+ onboard, of course BMC would be REALLY nice but maybe there's an X1 BMC card out there somewhere? Of course a PI and if BIOS /OSover serial could do that to a degree.
my jingsha has P2000 (x16/x16), m.2 1TB stick (x4), Asus quad hyper m.2 (x16/x4x4x4x4), Mellanox dual 10gb sfp+ (x8/x4) - it was fun figuring out how they broke all that down.