Why does the underside of this flip-chip BGA have small notches in it?
I think the links were to tie the pads together for plating. Every single pad once had a connection to the outside if I am correct. You can see traces going off the pattern on the top. After plating they CNC route out the connections. 

Many of the ball pads are tied together in groups for ground and supply rails so only single traces would be required for each group. 

Something similar is often done for edge connector pad plating- the connections are milled off later. I have also seen this on boards that are punched with holes to break the temporary connections.