In this context, I'd say PCH stands for Platform Controller Hub. Basically the chipset.
From what little information is given here, sounds like in the first case, the PCI-E lanes for that slot go through the PCH(chipset) rather than being connected directly to the CPU as in the second case. Will it make any appreciable difference? Probably not, though I'd need more information to say for sure. What is the context behind this/ where are these two terms written?