This is the best I could come up with so far.
A BP that holds the building piece, and has “arrow” components. The arrows obviously are not real meshes, so they aren’t included when the final building is merged to a static mesh. (Thankfully, when you merge a BP with other static meshes, even in level instances, it knows how to pull out only the static meshes correctly.)
Luckily, I think I can get away with only needing markers on things like roof pieces (which are really annoying to line up manually), and I don’t need them for all the walls as those are easy to place with a standard grid snap. A couple BPs for roof parts aren’t too bad.
I guess I’ll just wait to see if anyone else has any good ideas for editor markers.