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ALTER TABLE new_X RENAME TO X issue.
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Well, it looked like either a bug report or a variety of puzzlement.

Regarding "with time goes on, software's modern behavior will finally replace the legacy one", I think that legacy behavior has another 3 decades to go, based on claims made at sqlite.org and observed practices relating to backward compatibility.

I have seen that the SQLite dev team is quite open to consideration of improvements.  If you want to help in that regard, you would do better to suggest specific improvements, giving compatibility issues their proper due.

From how the ALTER TABLE change was explained and discussed in this forum, I can tell you that what it does is quite intentional.  If you have seen a doc error, you can do the SQLite user community a favor by specifically identifying it.