(1)
(a) Were the graphical glitches occurring during the lightning boot or afterward? I guess I wouldn't worry unless it carried on after the boot was done. Then I would suspect drivers. Anyway, it's good the glitches have gone. I hope the boot hasn't slowed a lot.
(b) That is right, is not good to have two system partitions plugged in at once. You may plug the SSD in only to quickly wipe it before a reboot. At least the System Reserved partition that is on it must be deleted.
(2) I wish you didn't have a dynamic disk (your Disk 1) mainly because I think it is an unnecessary complexity. I'm not sure it makes sense to have just one. I think it is a way to combine disks so that one partition can span the space on multiple disks. But your Disk 1 is 1 TB huge -- how can you need to grab more space than that for a partition? And/or one dynamic disk can be an automatic backup of the other & vice versa. I'd be afraid to do any of that, myself, thinking Windows can choke on it.
(3) Ah -- nice! Your recovery environment (RE) has gone into the Recovery partition on the NVMe, so says your ReagentC...!...
Windows RE location: \?\GLOBALROOT\device*harddisk6**partition3*\Recovery\WindowsRE
(a) I've seen it be more trouble to accomplish that in other threads. Test it this way: Click any Power icon, then hold Shift as you click Restart. It should reboot to the Choose an Option screen. Does it have the full panoply of options? For instance, there should be at least six at "Troubleshoot > Advanced Options". Then, get back to the first screen & click Continue to return to Windows. All is well with that, then.
(b) Referenced code in your BCD indeed loads the RE (WinRE.wim) from the NVMe Recovery partition. But there also is unreferenced code in your BCD to load it from C:\Recovery\WindowsRE. So, let's see whether there is a copy of it there too. Enter the following at an Admin Command Prompt...
DIR C:\Recovery\WinRE.wim /a <<<Does WinRE.wim exist there?
If that says, "file not found", (to be neat) let's delete the extraneous lines from the BCD...
BCDEdit /Delete {d3d6bda6-888d-11e8-a6a9-b3e2d28b7c04}
That's just to be neat. The lines do no harm since they are not referenced.
(4)
We want that 16 MB of unallocated space to be an MSR (Microsoft Reserved) partition. It belongs right there between EFI & the Windows partition. Although you boot & run fine without it, someday some feature of Windows (maybe BitLocker?) might want to use it. Or a 3rd-party software might want to use it. Here is what that looked like in DiskPart (when it was Disk 1)...
Partition ### Type Size Offset
-------------- ----------- -------- ---------
Partition 1 System 101 MB 502 MB <<<EFI. 101+502=603
Partition 2 Primary 464 GB 619 MB <<<Windows starts at 619.
Partition 3 Recovery 531 MB 465 GB <<<Recovery
Here is how to create the MSR...
DiskPart <<<Enter DiskPart
List Disk <<<Show disk numbers
Select Disk 6 <<<Select the NVMe -- IF it is still 6
List Part <<<Show its partitions -- should look exactly as above
Create Partition MSR Size=16 Offset=603 <<<Create MSR at offset 603
<<<It will occupy 603-618, inclusive.
List Part <<<Show the new MSR
Exit <<<Leave DiskPart
The 2nd List Part should show the MSR. Reboot to be sure the whole system knows it. It will look like mine...
It will be placed between System (EFI) & Primary (Windows) & will be type Reserved. I expect its partition number will be 4 before the reboot. After the reboot, I think it may remain as 4. That will be OK, if it does. The MSR doesn't show up in Disk Management. The 16 MB of unallocated space that is there now will have disappeared.