Hi! I'm also working on a map for a new project and I am absolutely no expert so maybe just a few things to consider??
For one I think it depends on how much the map will
be a part of the game. Like in metriodvanias like you said hollow knight or blasphomous the map displays every single room/section of the game since it is so neccessary for both exploration AND 100% completion since you use the map to see what areas you missed or parts you can come back to. Otherwise, games like Stardew valley have a more conseptual and less specific map as the world design is simple enough that after a while you rarely need to even use it to navigate.
So in your case maybe it seems like a more stylistic and relative map like stardew would be good? This way you could also design the houses/levels on the map in a more artistic and creative way than you could sticking to a strictly accurate map of your world. Ofc if that's not enough you could always have a more specific map of each level or something?
Anyways your post is from a while ago so maybe you've already figured it out but since I'm struggling with my own map layout I thought it might be kinda helpful to explain my own thought process with this
