I feel like my argument is not that hard to follow. I'm saying that just because machine-id makes fingerprinting easier, doesn't make it a bad decision because it could still lead to a net positive. In the Linux kernel's case, it might have been a simple solution to other problems, at a time when fingerprinting was not a concern. In systemd's case, it might have made it easier to accomodate legacy systems that depended on machine-id. Same with flatpak.

Linux, systemd, and flatpak are all fairly successful within their target markets. Clearly, you're going to need more evidence if you want to claim it's a bad decision.

In fact even if your goal is privacy and fingerprint resistance, just switching to another init system is not a panacea. First off, as mentioned in the flatpak github issue linked earlier, there are tons of other markers aside from machine-id that can be used for fingerprinting. And if you're using a mainstream distro, your new init system is likely less supported, meaning more bugs, worse security, and potentially a net loss in privacy.

Win the battle, lose the war. This is why I brought up compromise and strategy earlier.

In the end, it's hard to say how individual decisions like machine-id, contribute to the net result. There are pros and cons to each decision. Maybe if there was a competitor that didn't use machine-id and pulled ahead due to that decision, but I'm not seeing one.