Beyond the kernel, you have various libs and binaries that will be replaced during upgrades. All can usually/mostly be restarted without a reboot, but just upgrading packages alone won't guarantee all running processes have been updated.
As an aside, I just checked the geolocation server I'd setup for the installer.
03:14:51 up 1357 days, 3:43, 1 user, load average: 0.00, 0.01, 0.05
It's been up 4 years continuously on a Scaleway ARM box. I can't recommend them enough for such projects.
OS uptime gave me pride in the 90s. Today it's usually a bad sign.
And this isnt really the original Cray. Its someone who bought Cray and started using their name (although they kept the original location open.) So there is precedent. https://en.wikipedia.org/wiki/Tera_Computer_Company
I'm not aware of any supercomputers built by Lenovo. IBM has built a lot.
There are plenty of System X HPC installs. They just no longer come from IBM. Even when IBM still owned the line, it was being outsourced. The University of California SRCS system from ~10 years ago was an iDataPlex sold to us by IBM. Most of the boards had Asus marked on them.
Also remember the System X line was sold way after the Think lines.