That part of the exhaust will fit your car, all 96-00 Civics share the same exhaust from the rear wheels back to the muffler.
It's going from the rear wheels to the front is where it changes on some models.
What makes you think this is "probably" a Mugen?
The welds look really good and the one plate on it looks like it says "JASMA" on it, which Mugen exhausts have.
Though I've never seen this style of exhaust from Mugen, as it's not the twin loop, it's not the aero style either, so I don't know what model exhaust this would be from them.