Here is a picture of my HKS Hiper muffler. It also goes down to about 2.5". It is a baffle used to "catch" the exhaust and get more into the packing material. However, the HKS Hiper has a 3" inlet. APEXi N1s that I have seen are also like this.
Since I sell Exhaust Depot systems, I'll be asking them about this and maybe see if I can get exact specs on the mystery muffler.
If you decide you need a bigger diameter, I'll happily trade you a Megan Custom catback for that one, yours is worth way more. The Megans are truly 3" all the way through (you could put an arm through it, if you are skinny). However, they are loud because of that.