Thanks both for your suggestions
I'm still curious about this issue though,
Do you know what could have caused this difference in the distances between the left and right sides? I know the rigidity of convertible car chassis is smaller than "ordinary" cars. Could this just be "wear and tear"? Have you seen this knid of problems before?
I'm thinking about taking the car to a test center in order to check if the chassis is somehow twisted. Then I'll follow your suggestion and trim the rubber seal a little bit.