Nothing you reported is a problem or a bug. Over the underpass, it's normal you'll see some objects shining through, since the P3D graphic engine doesn't really support tunnels they are mostly faked, and will always show this kind of problems in a way or the other.
The problem in your 3rd screenshot is not a problem either: you are not supposed to go there with the airplane and, for the precise reason to allow SOME kind of multi-level simulation ( the airport does have multiple levels, including a parking area on an higher level than the mesh around it ), it's hollow in some areas which are, of course, all areas you'll never go to.