I’m new to the scene myself, and if I only needed two HDD bays for my build I would go with a i7 refurb Dell Tower (although I wouldn’t leave it on 24/7). At the most you may need to add RAM for your VMs.
I think that your question about Quickconnect can not be addressed here, but you should have a look at the MAC/Serial Generator Tool then make a decision on how to proceed. There are other ways to access your data remotely. Again I went with the default values, and the only feature that I am missing out on is WOL.
Outside of a Optiplex 390 and another build with a Asus e35m1-m pro my experience is extremely limited.
I never adapted the ITX standard, but if I were to do so I would start with quad core embedded solutions. There’s a chance that you may have to add a network driver.
Good luck with your build.