I will be the first to agree with you in saying that they do hang low. However, even though my 3.7" is tucked up quite close to the floor, due to the nature of a fat pipe it will still hang like dogs.
I bought a jap bolt on because it is exactly that - bolt on. No scraping, no knocking, no hassles. But I'm lazy.
That's not to say a custom one won't be better; if I had free reign ($$) i'd get a custom cat back made up in twin titanium 2.5" with twin resonnators, collecting into single rear muffler and twin outlets. Quiet, light, ultra free flow and excellent clearance.