The salesperson explained that leather keeps much warmer, but has no effect on breathability or water proof-ness.
Well he's not really correct there, so breathability is based on the concept that moisture will pass from a high saturation of moisture (next to your skin) to a low saturation of moisture (the outside). The temperature is also important, the high saturation area needs ot be a higher temperature to the outer (that's what the DWR helps with in a goretex jacket)
The Goretex material facilitates these process with pores that that allow water (in the correct state) out but not in. So if the water is trapped inside to the goretex layer (i.e by the outer fabric) this will obviously lower the ability of the moisture to pass though the goretex layer and therefore make the boot less breathable.
Leather is not as breathable as fabric. Air/moisture, etc. does not pass though leather as well as fabric. It is breathable but not as breathable.
If there was a
"pocket" between the membrane and the outside shell,
which I don't think it does, this is going to become saturated fast, and if it's saturated your boot won't breath. This is what a vapour barrier is but that works totally different to a breathable shoe.
So I would suggest that breathability is going to be better in fabric boots than leather ones. That said, he is correct that leather is warmer, so it's a a balancing act, warmth vs breathability. How much this is effected is debatable but it will have an effect.
He is correct that the outer has little input into the water proofness of a gore text boot, that's what the goretex layer does. Obviously there are differences between goretex boots.
TL;DR: he was making it up...