Deleting important data without warning is not the same as not providing a feature users might want.
It's a feature most software doesn't even have, and it is off-by-default. If you rely on your undo history to store "important data", you are doing something horribly wrong - to the level of storing your critical emails in the Trash folder.
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.
There is a flip side to this - is vim encrypting this data it keeps forever? If I delete something I consider sensitive, I might unwittingly be recording that presumed-deleted piece of data to my user profile somewhere to be deleted never.