My bro bought one of those Nyko Intercoolers not that long after purchasing the white OG 360 model, since he had read about it's heat concerns. While after over a decade of casual use, he finally got the RROD, but I don't think it had anything to do with the Intercooler. A bunch of the capacitors were blown and worn out and needed to be replaced. After reading about the caps, which there wasn't much info, it seemed like they were a lower grade product, which a few online with repair experience had said were more rare to find in 360's as though they were only used for a limited time for whatever reason.
It fired up right after replacing the caps, though both the internal fans weren't working, even without the Intercooler. I would've assumed the system wouldn't allow it to run like that in the OS menu, but it did. Since the Intercooler provided plenty of cooling itself, I just cut the internal fans out of their housing to remove the blockage, allowing for better airflow. I also cleaned out some minor dust, replaced the thermal paste, extended the heatsink shroud, etc, and it's run great ever since.
The exhaust was quite warm but not hot, which it should be, because the heat transfer efficiency is higher now with new, better quality paste. Plus better directed heatsink airflow. Though how hot the exhaust feels, will also depend on how much air is being pulled through the system. The higher the airflow, the cooler the exhaust will feel, in comparison to lower airflow and hotter exhaust. The Intercooler moves quite a bit of air, so the exhaust will never feel hot. Along with that, the higher the airflow, the faster the fan has to run, so the louder the noise levels. The Intercooler has tiny fans that run at high RPM which are loud and make my PS4 seem reasonably quiet.
That's way over a decade running with the Intercooler, so I'd assume in your case that it was either a bad batch of Nyko product, or MS was using that as an excuse. 360 had a ton of issue's that they obviously didn't and don't want to admit to in detail. They just paid to fix the problem while keeping the hardware issue's as quiet as possible.
They have heavily focused on fixing those weaker points of their XB hardware products ever since though. They clearly learned a lesson with 360, but also learned a lesson with XB1, that the answer can't simply be just make a bulky bland boring console, to house a bulky fan and heatsink to fix the heating problem. That lead to even better hardware in terms of the XB1S and especially XB1X.
If XBSX is running a little hot, the problem is highly unlikely to be another RROD like with the 360, it would be more of a long term RROD in terms of longevity possibly. Electronics are made to run warm in general, and can be designed to run hot, or even really really hot. That costs more though. They have to balance product cost and longevity, along with noise, etc, so it's a game of wait and see. Odds are by the time it could potentially be a problem, if that ever comes to pass, it'll be last gen outdated tech already.
Yeah, it was definitely the intercooler, I don't think Microsoft repair lied to me. They said that there was a power surge and told me to look at where the intercooler plugs into the power cord hole on the back of the 360, there were indeed scorch marks there from where the Nyko Intercooler power plug overheated. They said that because the intercooler draws power from the console power supply instead of having it's own power supply, it can cause major issues due to the amount of power that goes through the power brick, through the intercooler, and into the system, Nyko build quality wasn't great and could cause a short as that current passed through it. Nyko was actually sued over it as I recall because they didn't disclose to people that Microsoft recommended against using their Intercoolers, and they were forced to put a disclaimer on later models that they made, that you would be using the intercooler at your own risk of damage and warranty voiding.