my front upper moulding was done when the glass was replaced. It's much nicer than OEM -- nice and wide and looks nice. Others have done similiar....
Some else will need to comment on the rear hatch mouldings (think that's what you are talking about?) -- pretty sure there are issues there that require the glass to be pulled, but I'm not an expert on this....
On my Z I cleaned up and painted the upper rear gasket (black) -- came out pretty good! I used a dye (forever black) on the lower gasket (in the corners) and it also came out looking decent.