To my knowledge the windows have to be out so the headliner material under the seal. I suppose that it can be done by cutting the material and then tucking it into the seal, but the chance that it will blow out of the seal is greater.
That was basically what the guy was saying. I want it done right, I just wasn't anticipating the extra expense. I'm wondering if anyone has had it installed with the rear window in and how the results were.