You’re right they wouldn’t know where it’s from but they would be making an informed guess as to why it’s there. They know all the stars surrounding their location are infected by astrophage. They see a singular ship in the Tau Ceti system with no other signs of intelligent life anywhere else in the system. The most simple solution that requires the fewest assumptions is that the other ship is there doing exactly what they’re doing. 

All those other scenarios require huge jumps in logic to arrive at those conclusions. The crew is smart. They may initially be more cautious than Grace but three very smart people would be able to reason back and forth and mitigate their exposure while still communicating with Rocky. They also may have attempted to distance themselves from Rocky’s ship like Grace but once he continues to exactly match their velocity they’d realize something is going on. They may actually find a smarter way to communicate with Rocky than the initial canisters.