If you follow the orthodox installation, Slot 1 is where the software engineers want to see it. Its where most OS boots want to see it. If it isn't the weakest GPU in your card mix, why isn't it? Also assuming that you will be eventually installing more GPUs in the expansion box... be aware that sharing the buss will choke the GPU performance to the slowest card.
Evcen if you don't use an expansion chassis, flipping the hierarchy between slots may start inspiring some flaky behaviour with the rest of your software complement, simply because applications need to re-think their internal routing. One of my machines has a Titan GTX in slot one because its a double-wide card (and of course it remains unconnected to any external monitors) with the GUI -- a 4000, in Slot 2. It gets worse, because the Titan only runs under the Mountain LIon boot, and then if I flip back into Snow Leopard, sometimes the poor thing gets confused. And people want to flip the DVI cable into the slot 1 card... eventually you end up with a system that only you understand, like the messy office where ony you can find things.... and... then you can't.
Personally, I hate going off the script. Improv usually gets you "Lost" in the southern IO.
"I always pass on free advice -- its never of any use to me" Oscar Wilde.