It shouldn't really cause any issues as is, just harder to replace pieces when they go bad. When I replace a muffler, I don't try to save the tail pipe, I just put all new stuff on. I always just run the exhaust what I buy it with until it fails due to corrosion. Then I typically upgrade with a cat back system, which is always a different length muffler - but I buy stainless mufflers (usually $70), and aluminized tails.

He'll be ok for a while, but next time, go for a catback system that is made with quality materials...and consider installing it yourself. These muffler shops almost always use standard steel components that last 2 years in the rust belt - if you're lucky.