I think I say "couldn't" in this context more often than "can't". The two are virtually identical; however, "can't" is more objective and concerned with the laws of logic, I would say.
"He can't have seen the movie" sounds like a detective's remark, a logical deduction from other evidence in the case, and so does "He must not have seen the movie", another equivalent!
![Smile [:)]](/emoticons/emotion-1.gif)
.
"He couldn't have seen the movie" sounds more everyday, and slightly more tentative (or conditional?) in view of the fact that "couldn't have" can mean "wouldn't have been able to". "would be" is always more tentative than "is".
That said, you will hear all of these in various contexts. They all say that it is not possible that he has seen the movie, or that the only logical conclusion from the evidence is that he has not seen the movie, which amounts to practically the same thing.
Your other pairs of sentences can certainly be analyzed in the same way.