The one that covers the whole backseat, or just the part behind the seat? If you are talking about the cover that just covers the top and not the whole back seat, then yes that fits in my trunk, and mine is a 98, so it should fit in your trunk.
I believe the 1999-2004 tonneau that comes with the vehicle, which is a covertable boot does fit in the trunk. Now if your talking about the 2 seater tonneau, such as the Saleen Speedster 2 seater cover, well that does and will not.
One of my buddies here locally has an 03 Cobra and she ordered it, and had not but complaints with fitment issues, and this was even before she added a lightbar. Good thing you didnt order it, she shipped that pos back.
I'm dying down here in FL, it rains at least once a day and I'll be damned if I'm gonna get stuck with the tonneau while cruising.. so I'm SOL until fall.