Switching to WAL already makes handling Sqlite databases much less convenient, since you now have three files instead of one, and need a filesystem snapshotting mechanism to reliably back them up (so you don't have one state in the database and another in the wal). Making the filenames and number of files less predictable would make that mode not worth it for many use cases
Besides, even if the database is single-file it's still necessary to use filesystem snapshotting for live backup, or it's likely to get an inconsistent copy.
Never saw it myself, so I have no idea what the cause was.
VACUUM INTO?
Instead, sqlite provides an online backup api specifically for creating backups. This also takes wal mode into account.