OK, here's the deal, and this is exactly what I expected.
First off, the actual speed of the m.2 slots themselves are...
m.2 slot 1 - x4 speed
m.2 slot 2 - x2 speed
This is why the MB states to use PCIEx4 mode on m.2 slot 2 to get x4 speed, because it's the only way to do it. However you DO use up a 2nd SATA port doing so. Some people run two m.2 drives in RAID, each at x4 speed, but it takes up 3 SATA ports to do that.
The guy I spoke to checked with a tier 2 tech to get this info, whom also verified the best way to run one m.2 drive in x4 speed is on m.2 slot 1 using SATA mode, because it only disables ONE SATA port, which is SATA port 1.
What those guys are saying on the forum is totally wrong. I don't know why they would even think you could install an m.2 drive on this MB and get it's full x4 speed without using any SATA ports, because the manual clearly states one or two will be disabled depending which m.2 slot you use.
Also, m.2 slots are just short Pci-E slots. They generally configure them the same way the longer Pci-E slots for GPUs are, whereby the first slot is always higher speed. There are only so many Pci-E lanes supported on a Skylake MB made for Coffee Lake though. It's limited to how many lanes the CPU supports. This is why high speed drives like nvme drives require SATA bandwidth as well.
To do what you want to do (run an nvme drive at x4 without taking up any SATA ports) would probably require using the more expensive X99 platform, which supports more Pci-E lanes. Personally I think it's totally acceptable an m.2 drive with 3 to 4 times the speed can replace my old Plextor SSD that is only 500Mbp/s read, 365 Mbp/s write, and use no more than the same SATA port it's on.
Btw, I asked the tech I spoke to if he could send a suggestion up the chain to make it more clear in the manual what speed each m.2 slot is and that you can get x4 speed by only using 1 SATA port on m.2 slot 1. I told him the way the manual is written is causing lots of confusion. He said he'd pass it along. However ASUS are by no means the cause of or responsible for wild forum assumptions of being able to run an m.2 drive at x4 speed on this MB without using any SATA ports, which is why I LOLed at your trusting that chat you found.
The only thing confusing to me as I said is from the benches you posted, you appear to be running at x4 speed, because Samsung's specs on that drive are 3200 read, 1800 write, and you're getting close enough to that to verify it's at full speed. I would assume the reason your BIOS can only be configured to x2 on m.2 slot 2 is that it's actually an x2 speed slot. However it has to draw that power from somewhere, and running it in PCIEx4 mode should, as the manual states, disable SATA ports 5 and 6.
However IF you really are running at x4 speed, your boot times should be way faster. Check to see if you might have some security software running a scan at bootup, or the BIOS running some checks.