Slot 4 has a 16 lane physical connection It does not necessarily have 16 lanes of bandwidth.
All the slots (except slot 8) are physically x16. Slot 1,3,4,5 are electrically x16.
If can't physically get tot he slot in no way is 8 lanes of bandwidth doing "down the drain". If have populated slot 1 with a full height MPX module then 8 lanes of the bandwidth that that slot 4 was sharing a pool with is going there. That is already gone before even populated MPX bay 2.
What slot 4 pragmatically allows is to hook a phys x16 card to a slot that probably provides less than x16 worth of bandwidth. How much less depends upon what is in the other slots but nominally is the less than x16. If populate most of the slots in the Mac Pro ( or just put a heavy x16 consumer into slot 5 ) and the bandwidth of slot 4 simply just goes down in vast majority of configurations.
You are saying that slot 4 looses lanes when using a full height MPX module in slot 1. That is not logical.
Compare pictures on page 11 of the
Mac Pro Technical Overview and the apple support document at
https://support.apple.com/en-us/HT210104 to see how the lanes of slot 2 and slot 4 change when a full height MPX module is installed in each slot. The Apple support document shows a half height MPX module in slot 1 (slot 2 gets 8 lanes and slot 4 gets 16 lanes). The Mac Pro Technical Overview shows two full height MPX modules in slot 1 (slot 2 gets zero lanes) and slot 3 (slot 4 gets 8 lanes).
1) A full height MPX module (Vega II or Vega II Duo) in slot 1 uses all 8 lanes of slot 2 for the two Titan Ridge Thunderbolt controllers of the MPX module. A half height MPX module (580 Pro) doesn't have Titan Ridge Thunderbolt controllers and therefore allows 8 lanes for slot 2.
2) A full height MPX module in slot 3 uses 8 lanes of slot 4 for the two Titan Ridge Thunderbolt controllers of the MPX module. But slot 4 has 16 lanes, that leaves 8 lanes for slot 4. If the module were half height, then slot 4 would be usable as an x8. A full height MPX module might allow installing a riser cable if there is enough clearance. The cables at
https://www.adt.link/product/R83.html or
https://www.adt.link/x16.html are probably not low profile enough.
https://www.adt.link/product/R12SL-FL.html is lower profile but might also not be low profile enough (and it's only x1). Here's a post that discusses a similar problem (and has many pictures):
The notion of "snaking" cables under MPX modules is misguided. The design here doesn't particularly support that at all. I suppose someone will try to make it work in some happens to work hackery demonstration. It will happen to work, but not a particularly good 'best practice". if the MPX module covers it then don't use it.
I'm not saying one should do that. I'm just saying that it is possible. If a person needed those slots, then they should choose GPUs that are not full height MPX modules. If additional slots are needed, then a PCIe expansion box can be connected.
Maybe someone will create a method to convert a full height MPX module into a half height MPX module using a different cooling method.