Actually, I just made a points booking for this weekend and got two confirmation different numbers for myself and my wife—but I got two separate emails, too.

By the way, here’s how the single-itinerary confirmation looks in the email.
Regarding the third person’s check-in: that’s fine—we’ll have to set an alarm to check her in. Kind of an annoying return to the way it used to be. Even if we forget though, there being three of us, I doubt someone would opt to take the middle seat between two of us, so unless she’s relegated to deep C, we’ll likely have a row ourselves in any case.