Yes, since on the 1st slot, GPU can be utilized fully, due to the 16 PCI-E lanes the 1st (upper) slot has. 2nd (lower) slot has only 4 PCI-E lanes, where at most, GPU can be utilized 25% of it's max performance.
There are very rare circumstances why to use GPU in x4 slot, rather than in x16 slot. One of them being where x16 slot, for some reason, has died and you only have x4 slot left to use. But under normal use, there is no reason why to limit your GPU output to 1/4 of it's max performance by plugging it into x4 slot. There are easier ways to limit GPU utilization.