The top slot is PCIe 4.0 x 8, but it is a full length X 16 slot mechanically.

The bottom slot is not specifically mentioned in the service manual as being PCIe 4.0, so I am assuming it is PCIe 3.0 x 8, but a full length X 16 slot mechanically.

The information is at page 10 of this manual 

Are you sure a 3090 will fit in the bottom slot?  And if so are the fans going to touch the bottom of the chassis and cause thermal issues?  I mean I can barely fit a two slot card in there and that's after removing the caddies.

Bottom slot is pcie 3.0 x 8.

I gave it a go an confirmed with gpuZ its 4.0! it did fit with the sata racks taken out. Also unless you're water cooled on your gpu don't do this because there is 0 ventilation..

This is interesting, but I wonder if GPU-Z is having issues detecting it properly and indicating the incorrect value.

I have seen this before with the R10 board, and many utilities think it is a X570 chip set but it actually is a B550A.

If you would be so kind to also check with HwInfo64 and navigate to the correct bus, just to verify it also shows PCIe 4.0? 

I included screenshots of my R10, and it shows PCIe 3.0 for the second full length X 16 mechanical slot under HWInfo.

I circled the relevant information in red, and I have a SB Z card plugged into the slot where you have your video card plugged into.

You could always add Tall feet and cut holes in the bottom to allow air in.

"This is interesting, but I wonder if GPU-Z is having issues detecting it properly and indicating the incorrect value."

Yes, this is interesting, as the service manual lists only the top slot as pcie gen 4, and several other users have reported that, at least for the R10 v1, it was pcie 3.0.  Also, I'm not aware of any other OEM that puts pcie 4.0 on the lower GPU slot of B550A. Most do the top slot plus the M2 slot; however here the service manual and other users have confirmed the M2 is 3.0.  

If this is correct, perhaps it is an update for R10 v2.  The chipset doesn't support pcie 4.0, it is AGESA enabled (i.e., limited to CPU direct lanes) and the v1 and v2 R10 run off a different AGESA revision.  So that is another possibility, and Dell just hasn't updated the service manual to reflect the change from v1 to v2. 

I'll have to have a look there later on. I can't really boot up right now since I ended up finally adding up the active rear gpu waterblock and didn't realize I don't have another 2, g1/4 fittings.. So hopefully later microcenter here will. If it's only 3.0 will this affect anything? I don't have anyway to close the PSU anylonger with the waterblock fitting..

They do not run off the same AGESA version. The R10 V1 uses AGESA version 1.0.0.6 and the R10 V2 uses a higher version.

I forget what it was, but someone took a CPU-Z screenshot of it a while ago to see what AGESA version the R10 V2 uses. It's in some thread on here somewhere.

Found it. The TYROX R10 uses AGESA version 2.1.0. Picture V1 and V2 next to each other on this page:

AGESA versions 

It's the reason why I am fearing ReBAR support might not happen on the V1... Still waiting on tech support to get me an answer on it.  Fingers crossed.

I'm still waiting on Dell tech support as well.  It has been a pain.  They keep suggesting updating drivers and bios, even after we established that I have already done that...  They keep "escalating" it to the next level of of personnel.  I might hear directly from the president of Dell by the end of it.

Out of curiosity, are you using a Ryzen 3000 or Ryzen 5000 CPU in your R10?