Having built a few systems with bottom mount PSU's (including my own 800D and Lian Li's) I'd say the principle differences are:
1. Most modern bottom mount cases have divided interiors (thermal zones)- the "floor" of the main mobo compartment channels air to chipset/graphics card more efficiently.
2. Bottom mount provides better cable hiding and cable management (providing that there is sufficient room behind the motherboard tray and adequate cut-outs in the tray)
3. Centre of gravity is much lower
4. If the chassis has top mount fans then heat dispersal is good. A top mount PSU is ingesting warm air.
5. Most bottom mount chassis I've used have better clearance/less cluttered space above the motherboard tray, thus a better arrangement for larger aftermarket CPU coolers.
6. If watercooling, a roof mounted radiator is much more effective than a vertical mount-it will also make for a cleaner complete-in-chassis install -Assuming of course that the chassis roof is capable of accepting a rad.
That's about it.
BTW: If the bottom mount PSU chassis is a full tower then checking out the cable length for the motherboard 24 pin and EPS 12v on the PSU before final install could be an advantage.