Yes, and the result shows. The commentary track does indicate that they try to have a level of consistency between the theatrical and EE cuts so people seeing one version won't need to have prior knowledge of a previous film from the other edition. Therefore the scene involving Sam's use of Elvish rope in the opening of TTT was cut in the theatrical cut since the gift giving wasn't shown in the theatrical cut of FOTR.
They might "size up" Merry and Pippin for the extended edition of ROTK, but then again, they only grew a few inches taller in the movie, the growth wasn't as dramatic as in the book.