It really isn't that easy. You can make it work with a lot of hassle, and you'll lose nearly all of your OC headroom in the process due to the upper card suffocating in heat. That's the entire problem with mGPU and open air cards. IF you can get it to work (and you can't in all chassis'), you're compromising on overclocking. You will have to run stock or close to it and likely with fan speeds at high levels on both cards. And the temps on the upper card will still be high due to the lower card pushing air up towards it. I have tried this a couple of times and made it work, but it was not ideal at all due to the clockspeeds and fanspeeds being compromised because of the aforementioned reasons - and this is with a 350$ Cosmos II E-ATX case with like 12 fans. I couldn't imagine doing it in a mid tower or something along those lines.
So you're basically offsetting the benefit of an aftermarket card in the first place. Overclocking. You won't be overclocking much with open air cards if they're sandwiched. If at all. And in smaller cases it just won't work. Basically, reference is just less headache for sandwich CF or SLI.