Hey all,
Thanks to dabo13's help I've sorted out the duplicate prefab name problem. Unfortunately this means any previously-placed buildings will disappear (if they haven't already), but now all of the variants should load. Apparently the Steam Workshop version of the asset bases its name off of the asset name, not the file name, and I was using identical asset names. I've verified that it all works now. (You may need to unsub & resub for this to take effect.)