You make some valid arguements, but seemed to miss the points I was trying to make in several places.
In my first point, I'm asking for a darker, more domineering pc build. Yes, the new npc's are technically slaves, so why on earth do we have to make them fall in love with the pc in order to build our harem? Fear of punishment based obedience is a real thing, just look back a couple hundred years to see what I mean. Sure, it brings a lot of negative conotations with it, but it would be a more realistic approach that people may want to take part in.
In my second point, that's what I mean by mechanics. Having the ability to select a position or skill that the PC character has learned to automatically select said character for interactions while making them the dominant partner would make it both less resource and time consuming to be able to do specific actions with a new npc. Having to wait weeks at a time to find a book to teach said new npc the position or action desired is incredibly tedious, and the supply of said books in the first place makes it near impossible to stockpile them for later use.
My third point is being able to take more direct action when an invasion happens. In real life, if someone breaks into your home, are you simply going to sit in one room patiently waiting for said invader to find you, or are you going to be proactive in engaging the threat? I have a dungeon layout that forces invaders into a set path to be able to make it further in, but it would create build diversity instead of one snaking hallway. Also being able to send a unit to find and intercept the invader means you no longer have to have npcs stationed strategically yet unproductively in the way to slow down the invader.
Point four you seemed to understand my concerns spot on, and even added to the suggestion. Thanks for the improved ideas!
Point five was apparently also well received, so thank you for that. It took me a while to figure out how to even get to the market, and even after I had found it, I immediately forgot again as I had stumbled across it by complete accident and spent almost ten minutes trying to find it again after I closed the window. The controls could also use at least a hint or tutorial in the menu, as well as possibly enabling some way to change keybindings so that you can open the market or alchemy by mapping it to a specific button.