The one I got was the same way. Sorry but I didn't take photos of that stage of the project so I cant show you. My experience is "bolt on" anything exhaust usually needs some modification.
This is back yard red neck advice but I cut mine down with a reciprocating saw flush with the flange surface with a lip to hold the gasket. (not cut down to the gasket mating surface.) If you're not comfortable with that because its easy to mess up take it to someone that knows how to do this stuff. Though they're probably just going to cut it down too. Or weld a new flange on witch would be the best way because it would get everything lined up straight.
May have to just take an angle grinder to the lip of the OEM catback, I just really really hate making permanent modifications to the stock stuff.
Will post updates when I get the replacement order.
Anyone know how much a OEM 2nd cat costs? Probably expensive...