This clunk you are talking about is normal on honda transmissions. Every honda I have ever owned does this when going from park to drive, or reverse, or from drive to reverse and vice versa. It was there on the 6 speed, its here on the 10 speed. And last accord 6 speed lasted till well over 100k miles of brutally abusive canyon driving (coupe v6 is fun). This clunk also persisted on my Honda odyssey 5 speed and accord 4 speed. So this is all nonsense and paranoia from a young person who knows nothing about cars and has very little experience. No offense mate, but you just replaced a perfectly normal transmission. My 10 speed has less than 15k miles on it, and even reviewers noted that the transmission has a 15-20k mile break in period for gear 1-3. At slow speeds it does jerk/clunk/get confused as to what to do, heck, even my 2019 camry xse does it. Every transmission with more than 6 gears does this that I have driven (sonata, k5, accord, camry) its one of the first things I do when I test drive a car is to see if anyone has figured out wtf they are doing.
Yes. My 10 speed (2022) has the same exact issues you are talking about, I simply adapted my foot to the transmission and voila drives smooth, simply need to learn to drive. Had to do this with every new car I owned. YOU adapt to the car, not the car adapts to you. Its a heap of metal, it will not bend, it will only do what it can.
Also...NEVER....EVER... do a transmission flush....EVER. Drain and fill only. I remember that this was even recommended on the old 6 speeds, that you should never flush, you will destroy your transmission (or at least increase the risk of doing so). I will say that I drain and fill all my transmissions every 30k miles. This is just standard practice if you ask the transmission manufacterer. Auto makers simply don't list it as a requirement because they pay taxes on the oil and emissions of changing the oil, so if they recommend it, they pay for it. Hence the 10k mile oil change interval unlike it used to be 5k miles. I recently posted my oil results after 2k and 4k miles. Its not good. So go check it out.
0w20 vs 5w30 Oil Results - Accord 2.0T
If you don't want clunks, should have bought a toyota, I know I did, because they are just smoother although less sporty.
How to reset the transmission: Disconnect the battery for like an hour, or touch the + and - wires together with some copper (you wont hurt anything) this should reset the ECU and TCU.
EDIT:
you can find plenty of evidence to my claims on youtube
My 2011 Honda accord makes this noise after shifting the gear to reverse
www.youtube.com
EDIT2:
Here is what car and driver said:
Practical, enjoyable to drive, and with almost no issues, our Honda sedan is hard to fault.
www.caranddriver.com
"Other gripes were mostly isolated to the Accord's aluminum hood, which fluttered and flapped at highway speeds, and the 10-speed, which doled out harsh one-two shifts for about 15,000 miles before finally smoothing out. Honda said that roughness from the transmission was unexpected, but we weren't alone in this observation. One reader emailed us shortly after the purchase of his own new Accord to ask when he could expect the car's shifts to even out. "
This is why I tell every single person that if its your first new car, just buy a freaking toyota, because everything else will feel like its broken. Especially if you are NOT okay wrenching on your own car. If you refuse to drop your own grear box, just don't buy anything except a toyota. Every single car, including a honda, will require some work. Timing belts on the j35, valve adjustments, etc etc etc. Just buy a freaking toyota. This isn't anything against OP, its just my rule of thumb. My first car was a toyota and I learned how to safely work on a car by my self because the car was just hard to brake. Now many many years later I am comfortable with just about any car.