Instead of an alcove, it would be a counter with iron bars and the "npc" would be a static part of that asset (like in the old dungeon crawlers, where approaching the shop would open a 2d graphic with a picture of the showkeeper and a trading ui).
The trading itself would be handled via script. If you place a currency type item (like a custom "gold_coin" item) in the alcove/shop, the item would be replaced with the item that is sold by the shop. So you could have a potion shop that trades "gold_coin" for "potion_healing" or a bakery that trades "gold_coin" for "pitroot_bread".
Here is an image to give you guys an idea of what I am talking about.

EDIT:
I just found an example script in the "EDITING SUPERTHREAD"! So it is just waiting for an easy way to open the .model files with a 3d Software now!
-Geistertanz