Mainly cryptographic keys like the SSH host key, or stored RNG state. But this can very easily be mitigated using `cloud-init` or similar.

I'm not sure if they actually share /usr or unconditionally rebuild it on each device (after all, they do need to handle different sets of installed programs).

But /etc/ and /var/ in particular need to be system-specific regardless (even though you may be used to thinking of them as being on the same filesystem as /usr/).

> But /etc/ and /var/ in particular need to be system-specific regardless.

System-specific bits like /etc/machine-id get created by the booted system; the installer doesn't need to create them.

You can just leave those entirely empty these days.