May I ask how you are implementing your tilesets into Godot? Here is a sample scene I've made:
All tilesets use 16x16px and the settings for the tilesets in Godot use a Texture Resolution of 16x16px with no adjustments to the Margins & Separation settings as seen here:
I see that you mention that "individual items not aligning with either the bottom/floor or the top/ceiling ", could it be that you do not have walls setup from the Infrastructure Tileset? The walls in my sample scene above are the pink borders. All tileset assets take into account the walls from the Infrastructure Tileset so without it, objects may look out of place like this:
Also, our timezone gaps are quite far so I apologize for the late reply 😅 If you'd like, we can continue our conversation at either my discord (username is netherzapdos) or DM me at Twitter. I think your proposal is possible for the space station, I can design a couple of new modular infrastructure tiles with a couple of exteriors and that should give a good amount of unique combinations so each space station looks different 🤔