I've had no issues with the clunk, my gears and all shifting is still strong (on hard acceleration is a little rough and it'll surprise the inexperienced, but nothing horrible). Although I make sure I come to a COMPLETE stop before shifting gears of any kind. I believe this was my original problem, and caused the tranny fluid to sort of 'age' prematurely. I had gotten the car when it was 42k miles old in 2010, tranny fluid was still bright red when I got the car. With 71k on it now, it's due for a flush.
If the tranny is only 94k old in miles, I'd say it's fine. Just if you're a real eager quick shifter and you roll when you're shifting.. the clunk might be from the wear due to that action. I'd just be sure the brakes are engaged completely before shifting at any point.
If the fluid is the cause, it might be due to the lubrication abilities of the fluid in the tranny/etc. But if you're not having issues with your driving gears, I'm not sure I'd worry too much.
I do recall if I'm shifting to park on an incline of any sort, it tends to be a bit louder and/or the car will rock a bit along with the clunk.