Are you talking about the blue padded cases? Or the acrylic display case?
As far as the blue padded cases go, their later items didn't come with them. So there was not a padded case for the Vader ROTJ lightsaber.... if I'm remembering correctly.
As far as the display cases go, the acrylic holders were specifically cut to hold the specific lightsaber. Especially for the Vaders & Luke ANH & ESB sabers, they're cut so the T-tracks have space so the saber sits flat.