Ultimately, the problem is much bigger than /etc/machine-id since there are dozens of hardware IDs on any PC that can be used by malicious telemetry to silently to uniquely identify and track you, and the only solution to this problem currently is to make sure you really trust any software you use.
Systemd, in particular, acts a lot like malware for Linux because if you try to reset your machine-id a long list of stuff that breaks in in it. You could make a cron script to reset /etc/machine-id every day, but machine-id is so deep in the stack that you’d also have to reboot to ensure it’s updated.
Yeah, I have a hard time understanding the justification for systemd. The only real argument I’ve seen is that it standardizes the process, but that could’ve been done as a spec where you define a common config format, lifecycle, etc., and then keep the actual utilities decoupled from each other, but behaving in a uniform way.