Yes I agree that the SFO check-in agents may not know the BA policies.

There is an exception to the IATA rules for Most Significant Carrier that applies to US interline itineraries, where if the first sector is a codeshare then the marketing carrier's policies apply. But those rules also say that the operating carrier is still free to decide which of the two airline's rules to apply.

Hence why the CS agent may have hedged their bets. I would hope/expect the bags would be checked through, but if it were me travelling on separate tickets in this particular scenario/itinerary I think I would ensure I was eligible to enter Qatar irrespective of the published baggage through check policy.