Which version are you using for both apps? (RoboFont, Prepolator)
I quickly followed your steps and I cannot reproduce this issue. Can you give some more detailed steps to reproduce it?
As default new fonts in RoboFont already has a “background” layer.The UFO’s RoboFont is generating should be compatible with Prepolator cause they are valid UFO2 UFO’s. The layer data is stored in the glyph.lib with a custom RoboFont lib key.
Superpolator will ignore the layer data and will also not add the masters glyph.lib to new instances.
thanks