I'm new to S3D but I think that your thought is right, that it does handle the "bottom layers" at "start printing at height"... as new bottom layers.
And this is right to my logic.
If you dont want it, then set the bottom layer settings or the infill so that it matches to the rest.
I know its a bit more to change (2 settings) but there is no way around.
To make it clear to you: what should anyone do, that needs these extra "bottom layers" on a higher started printed object?
If the software is changed the way you like it, then these people have no option to do this, just because you dont want to change 2 more settings
