Stack them sideways and get a patch panel.
No but I can confirm that both M.2 slots will work while the internal graphics card is in use. I'm not sure how many PCIe lanes are given to both NVMe slots.
I asked about this a while ago on a different sub before testing it myself:
I'm thinking of setting up a file server that just functions as a file server and has three NICs:
\- 10GbE NIC
\- 40GbE NIC
\- 1GbE NIC
If I am going to max out these connections simultaneously how low can I go in terms of CPU power?
Can I do this with a dual core Pentium? What about a i3-4350?
Have you looked into AMD EPYC?
There are regular deals comming from china with Supermicro Motherboard/CPU/RAM deals:
https://www.ebay.com.au/itm/134674563486
A setup like this will be a power hog though.
To control it from another room you would use the web interface of whatever OS you are using eg Proxmox. To turn it on you can use Wake On Lan commands/apps on your workstation/phone.
Check out a build video for an EPYC system here:
https://www.youtube.com/watch?v=aCrldtj9bGY
You have to make sure the cooler you use is rated for the CPU though: