What’s your OS?
As far as I see in the source, and from my build on Ubuntu, the switch is on by default; below is what I did (from my log for December 2022)
$ git clone https://git.savannah.gnu.org/git/emacs.git --branch emacs-29 --depth 1 emacs-29
$ ./autogen.sh
$ ./configure --with-native-compilation --with-tree-sitter --with-small-ja-dic
$ make -j$(nproc)
If SQLITE is not part of your Emacs feature, you probably do not have the sqlite3 library. Again on Ubuntu:
sudo apt install libsqlite3-dev
Use function sqlite-available-p
to check sqlite availability in your Emacs.