Either...
1) Unscrew the antenna mast before installing the cover, then reinstall antenna mast after removing cover.
Or...
2) Add a plastic grommet to the cover at the spot where the cover would rest on the base. Then the antenna mast can be passed through the grommet. I believe you can find something like the plastic grommets at either HD or Lowes. If not, do an internet search on "grommet" and you will find a resource. I have metal ones, but I doubt you would want a metal grommet coming into contact with the paint.
BTW- my VW Jetta antenna mast fits on my 968 antenna base, so the thread/mounting point must be common or universal. Whether or not you can find one that gives better reception remains to be seen. I did try the 968 mast on my Jetta as it was smaller and noticed no real change in reception, FWIW.