There was a good recent thread talking about possibly getting around this rule and since I've been pretty frustrated by the rule, it actually made me seriously wonder, why does this rule exist?

Is it a .bomb system limitation? If so, then why not just override it when requested? And why not fix it?

Is it to make the e-cert less valuable and harder to use? Then why bother issuing the e-cert in the first place. And it doesn't make sense--you'd still be able to book 2 people on the same flight and use the e-cert--it just makes it more difficult to administer your travel plans, check in online, be assured of being on the same flight in the event of cancellations, etc. because you'd just still book two pax on the same flight, use the e-cert, but simply be on different PNRs.

Other possible reasons...?