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With two MPX GPU modules configured to use x16 each, also block 4 slot spaces. I expect the top slot that’s occupied by the IO card to use lanes from PCH, not CPU. That leaves 3 slots for the remaining 32 CPU lanes. All this is assuming there are no PCIe switches.
Slot 5 ( where Apple canonically wants to place the Afterburner card ) probably has access to full x16 PCI-e bandwidth. ( when some of the other 6-8 slots aren't using it ).
If someone wanted to use Slot 5 for an external PCI-e enclosure connectors then could add more high power drawing cards that way to the overall system ( just not internally).
The I/O care is probably not using the PCH. One, the PCH has to have the T2 connected ( it has both SSD and Power Management IC (PMIC) duties). That is where Apple has put all the other T2 in Mac systems. So there isn't much space DMI bandwidth there at all.
Further more still haven't accounted for the two 10GbE connections. Those combined with be another x4 PCI-e v3 worth of bandwidth. If throw yet another x4 PCI-e v3 at the PCH you are basically at 3 time oversubscription on the DMI link. I don't think Apple did that. ( Wi-Fi aiso on the PCH. Not huge but yet another piling on of the oversubscription that likely isn't completely off in many contexts. ) And also may not have accounted for the "top" Thunderbolt controller either.
Apple probably put slot 5's x16 on a switch with a combination of some of the other x8's . And some of the x8s on a the same switch as the x4 slot 8. In the latter case a x16 that all of the thunderbolt controllers go through ( the two x8 worth on the two MPX connectors and the x4 along with the "alternative " x8 slots in the MPX bays that are covered up by MPX modules and not used at all. . ).
If there is a x16 to x32 switch, then the possibilities increase dramatically. With two x16 to x32 switches, it becomes almost unimaginable that you’d have a shortage of lanes.
Apple has far more lanes assigned to the sockets than they have lanes. It is matter of how many switches they have, not if they have one in this system.
However, if looking to stuff "full sizes" ( or large ) x16 cards the need lots of power folks will have to go outside though because power will far more likely be the limiting factor more than lanes once have two MPX modules in.
Double wide ( space/volume capacity) x16 RAID controller cards would also be an issue after the two MPX bays are filled. Something "thin" like the Afterburner card would fix though.