Yup anything in the M.2_1 slot will drop down to x8 link speed even a PCIe gen 4 NVME. I initially did my install like this and found my GPU stuck at x8. Had to move my NVME drive to get a full x16 lanes.
I couldn't believe they gimped that honestly the Z790-E is a damn $500 motherboard. Can't believe they locked that only to the Hero or higher end boards.
Well, I'm going to have to buy a new board because it's stuck at x8 no matter where I place my m2. Maybe there is a bios eating shopping it but I tried everything from pch configuration to x16 mode.
Have you tried it on just "load optimised defaults" in the BIOS? Also, you may be seeing a power saving mode. There's not much that actually uses more than 4.0 x8 bandwidth (even with a 4090), so you may just be seeing it in a low power mode. There's a button in GPU-Z with a "?" next to the "Bus Interface" which lets you run a test which should push the card into its high power mode for the bus.
For a single NVMe 4.0 drive on the Maximus Z790 Extreme, it should always go in M.2_2, which is the dedicated x4 storage lanes from the CPU. M.2_1 should remain empty unless you have a NVMe 5.0 drive and are willing to sacrifice GPU bandwidth for a moderate gain in peak storage speed.
Do a clear CMOS, followed by "load optimised defaults" after installing the drive in M.2_2. GPU must be in the top slot, as the 2nd GPU slot is always x8 (x16 is only available on the top slot). Playing around with BIOS configuration for the slots is more likely to prevent it running at full speed, in my opinion, as the automatic defaults should just work. If it's not working on defaults/auto, I think it's more likely something physical, such as a bad CPU mount or bad contact in the PCIe slot (e.g. due to card sag).