In a lot of states, NC for certain, at least as far as diesels are concerned, a turbo DOES meet the legal requirements as far as having a muffler installed - ie, you can run a straight pipe out the back on a turbo diesel and still be entirely legal.
FWIW, the original warranty (if anyone out there still falls under the original warranty) only covers the exhaust system back to and including the cat - it DOES NOT include the muffler - so you can do whatever you wish to the stock muffler without fear of voiding the warranty - but that's probably a moot point as old as these vehicles are now.
The stock muffler that came on the CRD's (at least the 05's) is the same muffler they used for the little 2.4 L four ****** gas engine - I've got a pdf of the exploded parts drawings for the 05 KJ's on my old computer, and the part numbers are an exact match. I looked inside the stock muffler when I had it removed and replaced with a straight-thru Aeroturbine - baffled and restricted big time, nothing but a soot trap.
As far as the cat - fail-safe bet is to leave it as-is - no telling what future inspection requirements will be - some areas that are "EPA Non-Attainment Zones" for air quality will do a full-up inspection of it, making sure the cat AND IT'S INTERNALS are still in place - other areas will simply verify by sight that the OUTER CASING is installed in the exhaust system, and people have gotten away with gutting the internals out of it and leaving the shell in place.