I guess the situation in this specific case anecdotally comfirms again that outstation agents have a lot more discretion than the staff in the call centres, but equally 3c4 states that it’s your responsibilty to make BA aware ASAP.

Realistically, I don’t think many people outside of Flyertalk consider the implications of booking on separate PNRs, most people will be looking at the lowest cost options. I wouldn’t say the person making the booking was “mad” to make such a decision unless they were reasonably aware of the possible implications, and I’d hazard a guess the vast majority of the flying public aren’t.