Is it safe to update system packages using an operating system package manager?
Yes, it is safe, and moreover, we recommend using package managers (for example, "yum" on RedHat-based systems, or "apt-get" on Debian-based systems) to keep the system up-to-date.
On Plesk Obsidian, it can be done in the menu Tools & Settings > System Updates.
If Plesk is installed inside a container, the kernel updates are not necessary - the kernel should be upgraded from the Hardware Node.
If Plesk is installed on a hardware server, the kernel updates are recommended if there are only vendor's repositories configured. Otherwise, if the custom repositories provide new kernels, it is better to have the kernel manually updated from the vendor's repository. The reason is simple: major troubles are caused by kernels with GRSecurity patches applied. Plesk is not designed for working with such configurations.