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.
I was agreeing with you. Systemd breaks unix philosophy. You know what else breaks unix philosophy? The Linux kernel. It’s absolutely massive. If you want unix philosophy, switch to a microkernel.
Also another commenter in this discussion pointed out that flatpak does not actually obfuscate machine-id. You can read the issue tracker here: https://github.com/flatpak/flatpak/issues/4311
Basically comes down to a design decisions from 15+ years ago, in things that flatpak depends on. This is an open issue to this day. Would it have been better for flatpak to have delayed release until this was solved, possibly remaining unreleased to this day? Meanwhile everybody would have to use regular system packages, which not only have access to machine-id, but also the entire userspace, with zero sandboxing. I doubt that would be better.