I know they can be changed, but as the OP stated, there are a lot more steps involved and no guarantee that the changes will stay as you are playing or load into the game after an update. After looking at the link provided in this thread (which I think was prior to removing the fill empty lots in game options):
"Most of the customisation options can be found within the Manage Households screen. By default, Neighbourhood Stories will be enabled for the Other Households tab and disabled for the My Households tab so you don’t need to worry about any of your played Sims being affected by changes you don’t want.However, you can customise this if you do want your played Sims to progress in life when you are not actively playing with them. At the top of each tab in Manage Households, there is a new icon for Neighbourhood Stories settings. Click on it and checkmark the Enable Neighbourhood Stories box in the menu that comes up. This will enable all potential life changes for all households within that tab but you can customise this, too."
This was directly copied from that post on the neighborhood stories update March 16, 2022. It clearly states that it is enabled by default for all other households that you as the player are not playing. It further states in that post that in order to customize what stories affect which households, it has to be done individually.
As I mentioned before, there are approximately 93 premade households and not in world Sims in the start of a new game with all packs installed to date. There are also approximately 117 empty lots, empty apartments, and empty homes at the beginning of the game that according to @VeeDub you would just have to go into each one and eliminate (zero out) the beds in the lot info panel for all 117 lots.
This seems to be way more complicated and time consuming. I think they should have just left the option to fill empty houses where it was, and made the neighborhood stories for played and other households disabled by default. Let players decide whether they want to use the neighborhood stories or not and whether or not they want to have the houses filled or not.