I literally just finished working on my doors and windows today. Both the inner and outer rubber have felt on them. You should just go ahead and replace them both. The pic in your original pic is on the outer side, below the rubber connected to the outer aluminum trim piece.
Since the little connector piece at the top of the window that seals the top corner of the window and the top corner of the triangle window was broken I decided to replace that as well. Wow, what an ordeal. You have to remove the weatherstripping, the triangle glass, drill out the rivets, then replace the rivets and all the rubber. Take a look at
this thread - it helped me.
I have it all back together now, windows adjusted, triangles windows raised to fit properly, windows leveled, etc. You can adjust where the top weatherstripping on the Targa top sits with four screws.
My best advice is to gather your sources - the Bentley, "Sealing of 911," "Porsche Service School Targa Roof Repairs," and "Porsche 911 Workshop Manual" (I can send you a copy of it don't have one of them) - read them all, label everything as you take it apart, and be ready to spend some time. As others have said, Targa top and window adjustments are a black art.
Monday mine goes to get new door speakers and an amp under the seat before everything goes back together.
Good luck!