In cases where you have many user accounts on the same server(s) — HPC being a particular example —, Unix privilege separation is just one technical detail. The most important tools are the legal user account agreements and traceability after-the-fact. For example, if you ensure system logging is directed/tee'd to an otherwise inaccessible machine (and it includes authorization logging), you can always find out which process gained the extra privileges, and trace it back to the human user.
Also, things like CVE-2026-21988, where sufficiently privileged user within a virtualized container can acquire control over the entire physical machine, do also exist. Security is never perfect, just one step or tool in the overall solution. Honeypots, detecting script-based attacks at the outer edge of the network and blocking the related IP addresses for a fixed duration, are easily applied external protections. Tripwires, write-only logging, and even details like firewalling outgoing connections (as opposed to just incoming connections) work quite well as internal technical protections. With local human users, human solutions like clear legal agreements with legal repercussions work best. Trust is powerful.
I've been an University sysadmin for HPC and web servers, and designed a security scheme based on Unix groups (and default umask allowing group read-write access), and a small number of related utilities. Technically, it relies on basic Unix file access controls. In truth, it is based on humans being social animals: each file is "owned" by the responsible user account, with the project/conference identified by the group name. Nothing is anonymous, everything has your and your group's name on it. This is the key that changes how they treat the item and the security related to it: there is visible honor in behaving respectably. It works extremely well, because there is social cohesion even on the server. Just try it yourself: if you engrave your name on your tools, you'll treat them better, simply because they're no longer "anonymous", but yours, your name attached to them.