As far as I know, Fanatical is legitimate, and their deals are from taking a lower profit cut and passing on some of that to the customer. Steam takes 30% IIRC, so if you buy the Founders Edition at $130, $39 of that goes to Steam and Firaxis only gets $91. Thus Fanatical can offer it at 12% off at $114, still give Firaxis $91 (or even a bit more), and still make money, so long as their overhead costs are not too high.
Epic, by comparison, takes a 12% cut, so Firaxis would make $114.40 from a Founders Editon sold there, assuming no discounts. We can also tell from that that Epic can make things work with $15.60 in profits to cover their platform, which implies Fanatical can also likely make a go of it with $23 in profits.
So it passes the "does it make financial sense for them?" question too. Which is always good to think about when looking at discounts, if it looks too good to be true, it often is. In this case, Steam's 30% cut gives quite a bit of wiggle room, and as long as Firaxis still makes their $91, they have no reason to be opposed to Fanatical's discount.