I have found some infos. First: The things with the trees were just a problem on my hand. Second, I found out, that for some people it does work. For me, when I click on "break prefab" on the generator, it does clear the roads. Maybe its because it now realized, that something should be done. Its a very weird bug, if it even is one.

Update: If you want to select a single tree from that forest it is also not working. It's selecting the PolylineShapeEntity and not the one tree. It's making things pretty hard to do right now.