I have a newer seal (probably 15 years or older by this part) and it does the same thing. Rubs against the roofbox, squeaks, and stalls the door opening.
It would make more sense for this to be a 2 part seal. Once directly mounted to the T panel and a shorter / thinner companion on the door side.
You'd still get the same finished appearance / reduction in wind noise / water channeling, but without touching the body structure.