The adjustment to the kingdom rules for building-generated magic items to be below the settlement base value was a conscious design choice, mandated by the outline Paizo gave to the designer of the revised rules for Ultimate Campaign.
I’ve explained it before, but basically in the original kingdom building rules from the Kingmaker AP, magic item generation broke the system. Paizo made the choice to adjust it in two ways, the first being that Kingdoms cannot “sell” building-generated magic items for BP, and the other being to cap item values at the settlement base value. This was absolutely intentional and is not in error.
However... there are many players and GMs (myself included) who do not believe that the double whammy was necessary. Removal of selling items for BP actually solved the issue on its own. The only thing high gold value items from buildings means now is that PCs might be able to get some items sooner than the core game expects, but a bit of careful planning (and perhaps a friendly request for the PCs not to strip the treasury bare just to get that +5 vorpal greatsword for themselves) can mitigate it. The easiest way to manage it, interestingly, is to be hyper-strict with items rolled. Do not ever re-roll an item because the first one you got is “boring”. You get a lot of potions and scrolls. But that’s actually part of the balance.
So, my advice is to ignore the cap on the value of building-generated magic items, but be strict with what you roll - if that major item is a scroll of dimension door, that’s what it is.
This was exactly the sort of well reasoned with historical context answer I was looking for. It answered the underlying questions of why these things were listed this way. Thank you. This information should be listed on the PFSRD.