Actually with a board with a PLX onboard, you can have "88" lanes(40 CPU assumed + 48PLX), cause the PLX will enable switching around WHICH 40 lanes are being used at what port and the latency for that operation is so small you won't notice.
Virtually speaking, you'll have 40+48 lanes available or 5x 16x + 1x8.
The P9X79-E WS has a PLX and I hope the P9X99-E WS when it comes, will have the same specs, just 2011-3 socket and DDR4 RAM ofc.