Help Out A New Guy :P
The chance of memory modules from different identical memory kits not working in dual channel is very small. If you can't get a 4 module kit, just mark the sticks in 1 kit so you can distinguish the two kits and keep them together.
You large system will not work as desired. In order to use the DMM.2 riser x16 PCIe expansion slots may be restricted. My understanding is that with two M.2 ssd installed in the riser the two primary x16 slots would run at x8 and x4 respectively.
For the describe usage I'd suggest a 1TB M.2 NVMe drive and a 4TB SATA III ssd. That should be more than sufficient.
Consider using a single gpu in either system. SLI is not necessary given the monitor.
Configure the mini-ITX system with a 1TB M.2 NVMe drive and let it use the 4TB SATA III ssd in the main system.
Headless means without keyboard, monitor, or mouse.

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