Mini ITX - Headless Home NAS - with FreeNAS, iTunes, Plex
It depends what you are going to be doing with Plex. If you use the mobile phone streaming, that is a real time encoding that it does so you will want the extra power of an i3
As for the Node304, I have one for my Windows Home Server/Plex box and love it. Having worked with it, you really can't get anything smaller that will fix 6 drives without going to a Flex ATX PSU instead of a normal one. The Flex PSUs are never modular or as high of quality.
As for the SSD. I highly recommend still pursuing this. Even if not for the performance, simply having the OS on a dedicated drive makes future upgrades much easier. Trust me, having it separate when it comes time to upgrade the data disks having the OS and some of the data on the same drive is a huge pain, especially if there is any kind of RAID involved. You could get an adapter like this http://www.addonics.com/products/adm2px4.php and then use any standard M.2 SSD in it as an option. Here is a pretty cheap one that would likely be fine for your needs http://www.newegg.com/Product/Product.aspx?Item=N82E16820510043
The biggest issue with using a PCIe SSD is it means you will have to rely on software or motherboard RAID instead of hardware. Given that I think FreeNAS has a built in psudo RAID that lets you have redundant data with different sized disks, I would probably opt for that over a hardware RAID anyway.
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