A quick check of the parts fiche seems to show that this new muffler belongs to an exhaust set that doesn't have the rear crossover...
Does your bike have the rear crossover still?
Could just be that the new mufflers are built a bit differently and have a throatier sound than the NOS ones - seems the original part number is NLA.
If it bothers you, I would say get a new one for the other side and learn to live with your "meaner, grumblier" RT!
Current: 93 R100GS, 03 XR650R
Prior: 73 CB350, 77 R100/7, 83 R100RT, 04 XR650L
I love every motorcycle I've owned and even some that I haven't.