it was normal mode. I normally drive very smooth that is why I notice noises so easy.
Sometimes we drive slow until stop, clunk noise happens too. It sounds like the gear catch up to the next gear or down gear.
I agree with your concerns and have felt them too. Got 3K miles on mine (2019).
A couple of days ago, I was in sport mode. The street in front of me was wide open so I decided to have a little fun. Truck was fully warmed up. I didn't floor it but just gave it generous gas and got a huge clunk. I don't know if it was the trans or rear end because I wasn't expecting it. Could have been at gear 4-6ish. It was a severe jarring clunk. Unacceptable.
Every day, when I come to a curve and slow to about 15MPH, I get a clunk in the rear.
If I give too much gas after the first few minutes of starting, the engine will hesitate once. After that first, it's good. I tested this in manual and still got the hesitation so it's not the trans. The workaround is to barely hit the gas for the first few minutes of driving until you feel that first hesitation. The less gas you give, the less the jerking of your body from that first hesitation but you should be able to "learn" when it occurs.
All of the above was in normal mode except the one case I mentioned where truck was in sport.
As far as learning, the transmission doesn't have a positronic brain like "Data" from Star Trek. I suspect this is as misunderstood as anything else that people copy and paste.
A transmission is adaptive. Meaning, if you start it up and are driving easy, it will shift easy. Yet if you drive it hard, it will adapt to a more sporty shift pattern. As far as learning, you'll get 50 different answers, including mine: it will attempt to "learn your habits" within a short period of miles and likely not more than 1000. So yours should be done. Does this mean when you drive it shifts perfect and, your wife drives, the transmission goes nuts because she's hitting the gas at different points or beating on it? Doubt it. What then does it mean "learning"? I'll be honest and say I have no idea. Logically, I would think it will attempt to apply what it has stored in a ROM and if you're not matching that with the current driving pattern, it will adapt to match your current gas pedal patterns.
For me, it boils down to whether or not these clacks and clunks will do damage over time. I guess no one can really answer that.
Also, I felt clunkiness in my Dodge Charger. These trans have too many useless gears. If you look closely, in the Raptor, the trans often skips every other gear when it shifts. So not all these gears are practical for every day applications.
One thing you need to verify is where the clunk is coming from. All of my clunks come from the rear. That's the pumpkin, not the trans. So check for that.