Will a GIGABYTE GA-78LMT-S2 Motherboard be compatible with a RX 460?

Solution
Yes it's 100% compatible and here is some great info on 2.0 vs. 3.0 , virtually no loss in performance.
https://www.pugetsystems.com/labs/articles/Impact-of-PCI-E-Speed-on-Gaming-Performance-518/
Impact of PCI-E Speed on Gaming Performance