For UA-*A, it can be done within few mouse clicks, but for UA-UA it needs to be done in SHARES, experienced agent commonly works it around by adding a SFO-HND segment to your BOS-SFO record, print the tag and then remove that extra segment, or other way around(by working on the SFO-HND record instead) . In case the segment they are trying to add is sold out, that's probably why they mention"can't buy the flight".
Based on what you have mentioned, I feel the agent is pretty accommodating, at least the response is not "there is nothing we can do, go claim the bag and recheck it at SFO"