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In my opinion yes it should be covered by warrenty but this unfortunatly isnt always the case .the price sounds about normal there are alot of electronics in the boot .this is a mainteneance issue as drains should be periodically checked but if boot seal is damaged this could be seen as a wear and tear failure
I agree these should be checked at service
They either will or they wont there is nothing you can do to persuade them .they will descide if they feel that its within the cover of not