How to override /etc/systemd/system.conf?

In modern versions of systemd, it is possible to override the settings of the "default" config file /etc/systemd/system.conf with "specialized" configuration snipplets residing in files under /etc/systemd/system.conf.d/.

You could place your config line into a file /etc/systemd/system.conf.d/10-suppress-ctraltdel.conf, then it will be read when you reload the systemd configuration (or at next boot). To quote from the man systemd-system.conf page:

The main configuration file is read before any of the configuration directories, and has the lowest precedence; entries in a file in any configuration directory override entries in the single configuration file. Files in the *.conf.d/ configuration subdirectories are sorted by their filename in lexicographic order, regardless of which of the subdirectories they reside in.

Btw, this kind of configuration override mechanism is now the standard for many Linux services, so the approach discussed here should also work in other situations.

In /etc/systemd/system.conf.d/10-suppress-ctraltdel.conf, CtrlAltDelBurstAction=none must be in the [Manager] section (as noted in the manpage: "All options are configured in the [Manager] section"):

[Manager]
CtrlAltDelBurstAction=none

If a section isn't specified, the option might be ignored, as it might be in the wrong section.