We are talking about, at least I am talking about, 1964-1967 models only. The 1968-1972 models used a different set up.
The rubber on the outside doesn't actually touch the glass so it would not rub against the glass as it goes down if everything is adjusted properly. The rubber seals against the base section of the window assembly to seal out wind and water when the window is fully raised.
Concerning Repops brand not fitting one way: that doesn't really mean much, Repops are well known for not being correctly made. They are some of the better looking sets available and look more correct to original when installed correctly but they rarely fit correctly without a little help. Many people, myself included, have had to remove and reposition the retaining clips to make them work. That doesn't mean I put them on backwards, it means they were manufactured wrong. Never ever trust that a reproduction part is made correctly! No offense intended, just the facts.
And as mentioned above, the hard plastic block at one end of the long rubber ones for the doors are intended as a rub block. The block is to go to the outside rear edge of the window opening and registers against the frame that holds the glass when the window is fully up. This keeps the glass from vibrating. Also, this block has a small countersunk hole in it and should have a small screw through it to attach the rear edge of the rubber strip securely to the rear edge of the door.
Folks, if you have any doubt about which goes to the outside, just visit your favorite old car junk yard and check out the original GM window felts on any early (1964-1967) GM A-body. Rubber on the outside, fuzzy on the inside. Always.
If it will help, I post some pictures from my original body manual which also show which goes where.