Although there is no unwritten law about it, pant. puppets are usually taller. The reason is, being the reach of the puppeteer is extended with the longer arm, the body of the puppet must be porportioned. If it was the same size as rod puppets, the arms would be disporportionate to the body, and unless it was supposed to be a totally unrealistic character, it would looks wrong.
The Swedish Chef is taller technically. I believe they gave a higher lift to the other puppets when they had the Chef and another character in the same scene, or they lowered the Chef.
Ernie I know for a fact was intentionally lowered on SS. That is apparent on the Biography Close-Up with the footage of Jim and Frank doing a scene.
...now that I have shed my light on the subject, STOP FIGHTING YOU TWO! I'll send you to bed without supper, don't think I wont!!
-Matt