And f*****g magic.
Ok, so here's what happened.
I used a new USB 3.0 drive for the latest Mint USB install. Not only did it install, it also 'fixed' the enumerating drive process (don't ask me how) of the LSI RAID card on boot up, so that it would detect the drives in an instant instead of going one by one (no idea why it was doing that). I installed it, pulled the USB drive, rebooted, and was greeted by Mint.
Some fun things -> Mint wanted to know if I wanted to install alongside Windows Vista (?) during the setup process. I've only ever tried to install Windows Server 2016 on this machine...and I told Mint to blow away whatever the hard drive config it found. Additionally, I removed the SAS expander (as mentioned before) just in case, to do this install.
Anyway, I reformatted the same new USB 3.0 drive in Mint (haha) and put the latest MegaRaid Windows 10 x64 driver on it (removed unnecessary directories, because Windows Setup seems to get confused by a path of any depth...)...also, I formatted the drive in FAT32 (was using NTFS up until now).
I popped the Windows Server 2016 DVD into the DVD drive (as an aside, still needs to be secured...SuperMicro wants it on the back of the case, and I can't seem to locate / figure out the bracket...I may have lost some screws...), and used the driver on the USB keychain drive to see the RAID card (not that Windows won't let you try and write to it without the driver, apparently, with some success...then kick you out of the setup process...another little gotcha...gotta remember to load the driver first even if you can *see* the drives), and installed Windows. On reboot, Windows Server 2016 loaded.
As has continued to load. Been installing drivers, and applying patches (installing the Cumulative patch right now...going to see if the new MS / Intel Meltdown / Everybody Spectre patch accidentally gets applied and hoses the install. I've installed the MegaRaid Manager (I'm slowly transitioning to LSA...as soon as I figure out how to make it do something), and run a consistency check on the RAID-1 OS drives...they are consistent.
Some other minor things -> I've installed a Noiseblocker 50mm fan (the faster version, XS-2?) with some jeweler's cement to the side of the RAID card's heatsink to cut down on the temperatures. I've also installed one on the Intel 36-Port SAS Expander. They are now cool to the touch.
But yes, whatever Mint did, it seemed to reset the RAID card settings (or what have you). Now someone tell me why.