On my '07 the seat base lip has the molded in ridges relieved, and I have nevr had a problem. In fact I never thought of it in four years until reading this thread, and just checked mine. Its likely juat a tolerance issue on the fit. Looking at it, I'd trim the center of the lip as much as needed while still providing enough area/strength to hold the seat dowm. The right way to do it but a PIA would be to pull the rear plastic so you could see inside the airbox with the seat base on. As far as fixing filters, hot melt glue seems to work well on good clean foam.
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