They'll turn green as soon as the parity sync finishes, independent of the disks being formatted or not, though you need to format them before use, and that can be done at any time, before or after the sync finishes.
It should work fine but make sure you confirm by checking if the emulated disk mounts correctly before rebuilding on top, more details on the procedure here:
That suggests fs corruption, see if you can get the diags on the console by typing "diagnostics", then type "reboot" and if it doesn't do it after 5 minutes you'll need to force it.
This one should work in any board but it's for SATA m.2 devices, not NVMe
This one is for NVMe and it should work in a x16 slot that supports PCIe bifurcation, check board manual.
The problem is the way the RAID controller is identifying the devices:
Unraid considers that those 3 devices have the same serial number so you can only use one of them, see if that identifier can be changed or better yet don't use a RAID controller.
By default only 20% free RAM is used for write cache, after that you're limited by the device, you're also a little limited by network and/or shfs as initial speed should be closer to 1GB/s.
The original problem wouldn't disable disk1, that was something else you did, I'd suggest at least start with disk1 unassigned to make sure the emulated disk1 is mounting and showing the expected data, if yes then re-assign it to rebuild.
Never seen it before, just changing the Unraid IP should never cause this.
Do you have any VMs? No idea if it would help but you could try recreating libvirt.img but that would mean re-creating all VMs, though you could backup current image first.
If doing it then also look for the AMD IDE driver "pata_atiixp", since that one can be even more problematic, sometimes disks can't even be used in the array when it's in use.