It's partly a bug, internal and external resource buildings are meant to produce the same amount. This is a difficult topic, because we have two conflicting goals here. In the early game, the players' main objectives should be fighting for external settlements. If this is not necessary and you can get all the money you need from internal structures, the game becomes stagnate.
However, in the late game the focus should start to shift more and more towards outposts and finally siegeing the enemy fortress. Right now, though, games are simply won by one player capturing the majority of settlements and the other surrendering because he can't win anymore and playing out the siege would be pointless. For a siege to matter, the internal resource structures must produce enough that the besieged player at least has a chance to still win.
One problem here is that as the game goes on, the external structures actually pull farther ahead because you can upgrade those with the economy upgrade while internal structures often the command point upgrade because they're safer.
I'm still a bit torn on how to balance all these factors: Creating a progression from fighting for settlements to fighting for castles, making sure that settlements and map control are important, and making sieges matter. One idea was that internal structures cost 500 and produce 36, while external ones cost 250 and produce 24. That way, external ones would be more cost-efficient and you couldn't even build too many internal ones from the start, but in the lategame you could have a powerful economy inside the fortress that the enemy has to target to bring you down.
Another possible idea (which could work together with the first, but wouldn't have to) is to bring back the inflation mechanic, which means that resource structures produce slightly less the more you have of them. That way, we could slightly limit how much one player can pull ahead while still allowing them to gain an advantage over the opponent - you'd just have, say, twice as many resources instead of three times as much.