If those are the only possibilities, it would have to be the latter. This is currently be design but there is a feature request for Make2D to check the Show fills property of clipping planes in the display mode that is being used. I’ve added your vote to RH-33007.
Is there a way to make 2d for JUST the clipped geometry, as in not show geometry behind the clipped plane?
I feel that this would solve a lot of these issues. For reference examples look at SolidWorks and those drawing section options. This “show section cut only” is an option there and is often a better solution.