The 1500X is only better if you don't plan to overclock. The 1400 can be just as fast if you do plan to overclock. So that's up to you. There is the aspect of the 1500X possibly being a higher binned chip (meaning it passed a higher frequency test at the factory than the non X model), and it could possibly be more stable at a higher overclock frequency. At most it is usually 100MHz difference.
As for the GTX 1060 3GB vs the Gaming, that's difficult to say; because they've got a picture of a Founder's Edition GTX 1060 for the 3GB model, but the 3GB model doesn't come in a Founder's Edition. I would suspect they'd use the cheapest model they can, probably the Zotac Mini.
On the other hand, the "Gaming" model they have shown isn't much different than the cheapest Zotac Mini. They both have less than premium cooling, so they will run hotter than other models with dual fans or large heatsinks.
You could alleviate that by adding an extra case fan or two. I would probably choose the Corsair fans. It doesn't specify how many fans come with the case if you don't select any additional fans.