First off its common for dealers to repair or replace modified exhausts. Second of all take it to someone you trust to look at it, (they can check all fluids and filters and look for any more mods or previous areas been worked on), and should be able to tell you if it has factory tune if its a good shop, before you bought it. Was there a CEL on? The cars OE map does have some imperfections in it, I notice mine over 4.5k more than any where else. But they may have put regular fuel in it if they didnt know any better. Do you have a code reader any pending codes? do some research and get us some logs and we can tell whats going on.
In the meantime, bring it back and express your concerns to whom you purchased it from before its too late.