Obviously not all of them. But how come some penalties, which do not occur on the halfway line, are taken from 50 metres out. Explain please.

I think you are mistaken. Penalties are taken at the point of the infraction. Do you have any specific examples where this isn't the case in mind?

you might be mistaken, maybe the players look closer because of the angel of the camera when the penalty is given. Rugby games are shot using a wide angle lens, that causes distances to look a lot closer.