You can overclock with the NH-U12S-TR4, but it will hit thermal barriers sooner than the larger Noctua or the AIOs.
As for the Enermax units, the 360 will cool the best, then the 280, and then the 240. The 360/280/240 refers to the size of the radiator on the cooler. The larger the radiator, the better cooling it will provide. If you have room, the 360mm will cool the best, but it does take up a lot of room. You will need to see if your case will support a 360mm radiator, and then make sure it can support it with your preferred configuration. For example, some cases will support a 360mm radiator, but you will have to remove HDD cages in order to use it. You may need those HDD cages, so it just depends on the case. If you go with the Be Quite Dark Base Pro 900 it will easily fit the 360mm radiator. It is a great case.
If you go with a AIO cooler, you wont have to worry about clearances for GPUs or RAM. The AIO pumps have a much smaller footprint around the socket than a big air cooler. Where AIOs have issues as it relates to size is installation of the radiator. But again, with the Be Quite case you have chosen, this wont be an issue.
I think the 280mm AIO is a sweet spot for most cases as typically you wont have configuration issues with most decent cases and it does a good job cooling. I have the 280mm Enermax and at 3.7ghz under full load my temps are 51C.
As far as noise is concerned the case will play a major role in how loud your system is. Be Quite! makes some good cases and they are designed to keep sound to a minimum, but I cant confirm how it will sound because I dont have that case. I have a Fractal Design R6 and it is also designed to keep noise levels low and it is very quite with the Enermax 280mm.
Here is a good review of the Define R6, but you cant go wrong with Be Quite! either.
https://www.youtube.com/watch?v=WWaxLG2hCgo&ab_channel=HardwareCanucks
When you install your RAM and boot your machine it will run the RAM at 2666mhz as this is the native speed for Threadripper. So in order to get the 3200mhz speeds you will need to overclock the RAM. Pending on the application that you are using, running running RAM speeds at 3200mhz over the 2666 will make a big difference in performance. But in other applications, it wont be as noticeable.
The biggest issue with Threadripper and Ryzen for that matter is memory support. The Zen architecture has real issues with RAM compatibility. In fact, the reason I went with the ROG Zenith Extreme was because I already had the RAM and it was the only motherboard that I could find that it was listed on the QVL. Given RAM prices I chose the higher motherboard other than taking the risk of it not working.
With that being said, it looks like the Gskill Trident Z G.Skill Trident Z DDR4-3200C14 32GB kit is listed on the QVL. So it may be worth the risk because you will be getting the same RAM, just at a higher capacity of 64gb. If you do go that route, then make sure you get the RAM from a vendor that accepts returns, just in case.
There are several 64gb kits of 3000mhz speed RAM that are on the QVL, but I dont know how much they are because RAM prices are nuts right now.
Good luck man and I hope you enjoy it.