Why Do Pin Numbers Sometimes Look Like Reference Designators?
BGA packages have a grid of pins (hence the name, ball grid array) and so the names are more X and Y coordinates as opposed to simple pin numbers.  Generally BGA pins use letters for Y and numbers for X, skipping a few letters that look similar (I, O, Q, S, X, Z).  So pin numbers for large BGA parts that can be things like AJ22, AP15, C4, K9, etc.  

As for referring to particular pins, you could say one of the following: "U1 pin G5", "pin G5 on U1", or "pin G5 of U1".  You generally want to make sure to add the word 'pin' so that it's unambiguous.  Especially because you can have a pin U5 on U1 and a pin U1 on U5, if U1 and U5 are both in BGA packages.  Same goes for mezzanine connectors.  

For reference, here is the footprint for a Spartan 6 FPGA in a 900 pin BGA package: