I disagree. I had the entire exhaust system behind the crossover pipes replaced on my 95 SR a few years ago, which included a high-flow catalytic converter, low-restriction muffler, and 2-1/4" piping for $240. It fits well with no banging or clunking, has a nice aggressive sound and slightly improved the top-end power of the engine (as measured by my butt-dyno).

If your system has pre-cats then it would be a little more complicated and expensive, but still no comparison to what OEM parts would cost. I feel your frustration with parts that don't fit properly, but with a custom exhaust being fabricated a shop would be able to use aftermarket converters and muffler, so trying to make aftermarket parts bolt up to the factory exhaust wouldn't be an issue.

My experience has been that mechanics don't always recommend what's best for the customer's wallet, or for the vehicle they're working on. The mechanic's time and income is usually more of a priority, and if your mechanic doesn't have the equipment to fabricate an exhaust system himself he's going to recommend replacing the individual exhaust system parts rather than send your vehicle to an exhaust shop and lose the job.