How to create variations in commerce file?
The set up should be:  a single product display whose product reference field has both the (I'm assuming) Windows file and Mac file.  The relevant product attribute being that taxonomy term.  So, in your product type, place that taxonomy term.  It sounds as if you put that taxonomy term on your product display, which is a node type.
Note:  products entities = variations in Kickstart 2.  Products I believe refer to product displays.