The version according to the documentation [URL] is PCIe 2 x 4. It's interesting that your SSD is running at only 2 lanes instead of 4. Did you try updating the BIOS, checking its setting if there is way to update lanes from 2 to 4 and also the firmware of your SSD. I have a 3060 with Samsung 970 Evo Plus NVMe and it gives 1.8GBps of read/write on PCIe 2 and 4 lanes.
This is crazy, we bought some Optiplex 3060 units for work and I decided to upgrade one that I do dev and image work on to a new Samsung 970 Pro NVMe in order to enjoy all the benefits of 3000+ MB/s read/write speeds. But when I installed it, the read/write speeds were not much better than the old NVMe drive it replaced. So I did some looking in the Intel RST monitor and found this: PCI Link Speed: 2000 MB/sPCI Link Width: x4 I used some other diagnostic programs that rated it as PCI 2.0 x4 rather than the PCI 3 x 4 (up to 32 Gb/s bandwidth) specs found in the 3060 manual. Just to be sure it wasn't the Samsung, I also bought a top-end ADATA XPG SX8200 Pro with read/write specs of 3500/3000 MB/s but again these were around 1500-1700 MB/s benchmarked and all diagnostic programs also stated it was running on PCI 2.0 x4 and not PCI 3 x4. I tossed both of these in my new Latitude and using a USB boot drive (so as not to wipe the drives), both the Samsung and the ADATA showed PCI 3.0 read/write speeds ~3000 MB/s without an issue. Bam! Then I started searching online and found many others with the same problem with Optiplex 3060/5060 systems (while older 3050 systems seem to work fine), so I wanted to add my voice to the charge in getting Dell to fix this blatant performance issue.
Optiplex 3060 NVMe SSD Only Works in PCIe 2.0 Mode?