It doesn't sound like it's VA's fault (unless you mean they ditch one provider and jump to the other). From what I read they are two distinct computer systems, so one system knows nothing about the numbers in the other system, which both would need to do to link the reservations.
For them to connect would require that the providers themselves (e.g. Amadeus) link with each other but there's not a lot of incentive to do that and they either wear a big project cost themselves for fairly little demand, or try to pass it on to their airline clients worldwide, some of whom might then argue they don't need/want interconnectivity.
A similar situation was when the bank ATM networks connected with each other which took a while. However, there's a lot more bank customers overall who can be encouraged to switch, and fees are more readily charged in that situation.
Surprising that the ADL check-in lady wasn't more "book standard" and charged the excess there; if not for her misreading the PE allowances then at least for exceeding the allowance for DJ domestic PE (which, if the interline is set up correctly, would have also been incorrect to apply in this situation, since flights interlining to the US have the same allowance (the international flight's allowance) throughout the entire routing).
