The Linux version has only 1GB RAM and only 8GB onboard flash.
Basically, the difference in price between the two SKUs is purely hardware based. So, buy whichever hardware you need, and install GNU/Linux.
On a side note, I have an HP Stream 7 tablet with an Atom CPU and 1GB RAM, and it runs 8.1 very well. I'd imagine even the lower spec SKU of the Intel stick would run it fine. Storage space would be the only real issue for that OS.