With the amount of heat TR puts out, the size of an air cooler will take up pretty much entire mobo. Many small ITS systems already require low profile ram to clear the heat sinks. If you go water, you still need a place to squeeze the hoses out and all this vertical stuff gets in the way.
It's already an issue just routing wiring in many of these cases without disturbing airflow. Also keep in mind, this is a problem with 95watt cpus, I can't even imagine trying to cool a
Threadripper in my Ncase. If you need a larger case just for the cooling, why saddle it with a compromised motherboard.
If you want to see what you are facing here's my adventure with a "95 watt" 8700k in an Ncase.
Here is how tight an Ncase M1 with Noctua C14S fits, however you need to replace the 140mm fan with a 120 to even get this. While I didn't use a Noctua fan when I tried this I was uncomfortable with system temps.
Pic by M1AF on Reddit
https://www.reddit.com/r/sffpc/comments/ahn4e8/ncase_m1_c14s_stock_psu_mounting_it_fits/You can turn the psu sideways, but then you have this (most also mount dual 120 or 140s under the GPU and a 90mm at the back of the case, filling the case entirely).
Shot from the top
Pics from a user named Zoob, but closely match what my system looked like inside before I changed to a Noctua U9S.
https://hardwarecanucks.com/forum/threads/ncase-m1-v1.79119/The C14S ran fine when the PSU was sideways the problem is the PSU was sucking massive amounts of hot air. Under modest loads the Silverstone 450 watt PSU was running at or above recommended temps, and under full load, the heat and noise was terrible. Switching to a 650 Corsair helped, but even then I was pushing max temps while gaming. I switched to a U9S, which had less cooling capability, added an extra fan, and while it let the cpu heat up a little more under load the rest of the system, particularly the PSU, were kept cooler.
Understand, this is one of only about 3 coolers capable of handling an 8700k or 9900k in such a small box and those are 90-145 watt CPUs, Threadripper can reach 270 watts. Basically once you pass about 200 watts between CPU and GPU things get really complicated in terms of cooling. And if you think these cases are stuffed, the Ncase isn't even considered all that small these days.