Personally, if it's tight I don't care if it's flush or not.
Doesn't change the flavor or how it smokes.
I'd keep it.
If it bothers you consider it a lesson learned.
What bothers me faaaar more is when I buy a bent pipe and it's not bent straight.
That's a major frustration for me and one of the first things I look at when I get a bent pipe, which isn't that often since I prefer just about everything about straight pipes.