Imported objects and built in objects are respected by the drop from the sky builtin rocks, etc.
Unfortunately, that is not true with plants. Plants will grow out of imported objects and grow under builtin houses.
Trees tend to respect imported and built in objects.
If the rock layer is turned off plants will not grow out of imported objects.
Two side notes:
Please make the layer icons for land and water a couple of pixels thicker. to better see their status.
Right Ctrl Delete does not clear the scene on the default objects on FlowScape load until the Home/Settings menu displayed.