I think this could be mitigated by counting confirmations differently. We should think of confirmations as only coming from blocks following the miners' more strict rule set. So if a merchant were to see payment for the first time in a block that met their own size restrictions but not the miners', then they would simply count it as unconfirmed.

If they get deep enough in the chain, though, the client should probably count them as being confirmed anyway, even if they don't meet the client nodes' expectation of the miners' block size limit. This happening probably just means that the client has not updated their software (or -minermaxblocksize configuration, depending on how it is implemented) in a long time.