I don't think there should be a difference for a single NVMe when using PCIe 2.0 x8 (or PCIe 1.0 x16 if you have a x16 card) for upstream link because it has similar (or slightly greater) bandwidth (32 Gbps) compared to the NVMe's PCIe 3.0 x4 (31.5 Gbps).Btw, the Ableconn PEXM2-130 is a x8 card, the switch of the card is an ASMedia ASM2824 x8 switch, even with the Mojave firmwares installed on the backplane the maximum speed possible is around ~2800MB/s - even with a RAID array. This is a limitation of the PCIe v2.0 slots of the Mac Pro.
Only a card with a x16 switch will get more throughput, around 3200MB/s for a high end blade and around 5900 to 6100 MB/s for a high end RAID array.
I've done NVMe tests with various numbers of NVMe in an Amfeltec with different widths and speeds.
https://forums.macrumors.com/threads/amfeltec-x16-pcie-with-4-ssds-5900-mb-s.1936311/post-25247002
https://forums.macrumors.com/threads/amfeltec-x16-pcie-with-4-ssds-5900-mb-s.1936311/post-25252615
I would have preferred tests using AmorphousDiskMark.app or maybe ATTO Disk Benchmark.app which both can give higher numbers then AJA System Test Lite.app
PCIe 1.0 x16: 3045 MB/s (MacPro3,1) 3277 MB/s (Hackintosh)
PCIe 2.0 x8: 3270 MB/s (Hackintosh - to do x8 in Mac would require taping some pins)
I also did some tests in a HighPoint SSD7505 with multiple NVMe (using ATTO Disk Benchmark.app instead of a RAID) in a Netstor NA255A connected to the MacPro3,1 (PCIe 3.0 x8 slots with PCIe 2.0 x16 upstream)
https://forums.macrumors.com/threads/pcie-ssds-nvme-ahci.2146725/post-29483973
I also tried the SSD7505 directly in the MacPro3,1 slot 2 (without Netstor NA255A)
PCIe 1.0 x16: 3449 MB/s (MacPro3,1)
PCIe 2.0 x16: 6333 MB/s (MacPro3,1)
I've also attached some other tests with PCIe 2.0 x16 for the HighPoint SSD7505: