Sure thing!

Warnings will happen, but they are just warnings - if the tagging and geometry are correct, then they can be ignored. The iD editor is not very good with complex situations with levels and building parts and often complains about stuff and offers incorrect fixes. Technically, the points do not connect to the building, because they are on different layers (and obviously do not connect in real life), but this is when the editor starts complaining - it does not understand that a building part on a different layer implies that the building itself in that location does not overlap anything. Building parts in particular are complex, because they "override" the building shape, but almost no tools out there (except 3D renderers) really understand this.