All those things make the story and the exploration a lot less apealing to me because what I like the most in RPG is having the feeling that I'm living an epic quest in a believable world.
In BG3 everything feel divided in parts that are not coherent as a whole.
As an avid Dwarf Fortress player, I understand your point of view. I too do like very cohesive worlds, where everything is a believable cog in an abstract giant machine. Ultimately, I think it boils down to the dichotomy open world/theme park. The MMO world also had this fracture many years ago, they used to be like you described until WoW redefined the genre with its popularity. Both have their advantages and I believe BG3 fits comfortably on that scale. BG 1 and 2 were more cohesive in their approach, but I can appreciate the way this game tries to set its stage. Locations are nice, npcs are memorable, stories hooked me and I don't feel like I'm being taken out the experience by compromises on map design.
