Persistent undo exists to recover from an accidental write-and-quit mid-session nuking some stuff you really didn't intend to delete. If you care about its contents beyond a handful of hours, you either need to adopt proper version management, or start making backups.
Reading the PR the change was needed because the old undofile format was fundamentally broken. They considered making an undofile-upgrade mechanism, but it would've caused more issues that it would've solved. In other words: stuck between a rock and a hard place.
A duty of care also means occasionally having to break things to make it better, or else you end up being stuck with spacebar heating[0] forever. As a user it does suck, but that's the price you have to pay for using actively-developed software.