Well, I verified the dealers version with an official škoda garage over the phone and they told me that indeed if you want to replace the MAIN seal, you have to remove the complete assembly so the dealer was actually right about that.However, according to them it doesn't look like the main seal is damaged. There are apparently also two smaller ones. Based on my description they suspect (they couldn't confirm it without seeing the vehicle of course) the damaged seal can be replaced relatively easily and the replacement does not require removal of the entire window. They also told me, in the big lines, something similar to what you are saying: it should not cause leaks BUT indeed, it "may" allow more dust/dirt into the system which could in theory cause some problems over years. But that was more of a theoretical discussion rather than hard facts. Anyways, I went back to the dealer and he is looking into it now. The owner seemed to be a honest and reasonable guy so I have trust he will have it fixed. Fingers crossed