Hey Matt,
The LTR needles are made by keihin for the keihin pwk carb that you have in your bike. The part number is machined off to protect it from being copied; This accounts for the wear marks you see near the grooves for the clip. By the way, JD jetting machines the numbers off all their needles as well...
So, to answer your original question, no the LTR needle isn't softer than a keihin needle; It is a keihin needle!
The keihin pwk carb doesn't have a replaceable nozzle jet (where the needle fits into the carb body) - this is machined into the body of the carb. It could be this was a little rough causing some initial break-in wear on both the carb body and the needle; Or as Glenn said, you had some ingestion of dirt which caused some wear.
jeff