Undo files and persistent undo are not meant to work that way. They are just persistent across process restarts. That's all.
They live in ~/.cache which is defined as "user-specific non-essential (cached) data".
Despite this user's impressive résumé, they simply misunderstood the feature.
In what way is it not a process restart if I stop the process, install/upgrade NeoVim and start a new process?
What did OP misunderstand? I am not sure how and where their understanding of "persistent undo" is different from "persistent across process restarts"?