My advice to the guys who have not installed their cover yet would be to:
First, clean the area really well. blk88verde has a good process there.
Play with the positioning to get a best-fit to your roof.
Tape off your location with painters tape so you can fit it in the exact location you so carefully planned out.
Carefully remove the seal from the base.
Dry fit the naked cover to the roof and identify areas that contact the sheet metal first.
File those areas down with a fine file or dremel until you have a solid contact ring around the entire perimeter.
Clean the cover up with the same procedure as the roof.
Replace the seal to the cover.
Attach the antenna wire to the base.
Place the cover in the box you taped off when your originally fitted it.
Stick it down!
The 3m tape is good stuff, and if you give it a nice fit condition it will do a nice job for as long as you need it to. It will be able to absorb some of the deviation, that is its job, but do your best to make its life easy and it will treat you well.
UPDATE: Today i tried to refit the antenna cover. First thing I noted is that the seal does not come off the base very well, there was no good way to save it enough to be reuseable. Second problem I had is that when i went to remove material with the dremel, large chunks of paint came off. SO paint adhesion was not that great. Also, the antenna is very soft PVC or ABS. You do not need a dremel at all After seeing how much material i was moving I went to 240 grit sandpaper and that worked just fine and kept me from getting overzealous in the material removal.
I have contacted VG regarding a new seal and I have a very precise fit to my roof. After I repaint the fin I am positive I will have a good looking product, but I had to work much harder than I thought to get there. If you told me what a can of worms I was about to open, i would have left it well enough alone, or just left the thing off.