How does the Space Shuttle dock the ISS?
It looks like LEGO did not intend to make Shuttle attachable to ISS despite the statement. At least not with a stud-on-stud connection like the set is designed right now.

As seen in picture below, Shuttle is docked using a connection port inside storage bay with its doors open. Not sure if it is possible to replicate opened doors in scale Shuttle and ISS are built.



However if you neglect the lack of this feature and accept the docking with storage bay doors closed a little modification could solve the issue. Existing Fez piece attached to ISS isn't deep enough to accept Tile, Round 1 x 1 with Bar and Pin Holder (to invert stud to anti-stud) so an addition of Plate, Round 1 x 1 with Open Stud aka "Apollo stud" in between both of them will help modifying the docking port.