Rhino isn’t able to split the crossover edge and make two separate planar caps, so it makes a crossed over single surface. It says closed, but there is one part of the surface which is now considered a backface, so it is transparent. Fixable by first manually making one of the caps and joining (which splits the edges), then cap the remaining hole.
JoinCapBug.3dm (2.5 MB)
Or by using _PlanarSrf and window selecting the edges of the openings. Rhino is smart enough to spot the self-intersection and ask if you want to invoke curve boolean processing. That generates two correct surfaces.
Yes, my point was just that it would be nice if Cap was smart enough to do this without manual intervention.
Yes, I agree. And if PlanarSrf has the necessary smarts then it should be possible to make Cap cleverer too.