Is there a way to have SQLite read from ~/.config/sqlite/.sqliterc instead of ~/.sqliterc in accordance with the XDG Base Directory Specification?

Not currently automatically, no. The only workaround would be:

$ sqlite3 -init ~/.config/....

Which could be wrapped up in a script like ~/bin/sqlite3:

#!/bin/bash
exec ~/bin/sqlite3.bin -init ~/.config/... "$@"

That sounds like a good addition, though, and i have added that to my TODOs for the 3.41 release.

Is there a way to have SQLite read from ~/.config/sqlite/.sqliterc ... in accordance with the XDG Base Directory Specification?

Implementation question: are there any strong opinions as to whether it should be ~/.config/sqlite/sqliterc or ~/.config/sqlite3/sqliterc? My instinct is to use the latter. The dot in .sqliterc seems superfluous in this case. i.e. my proposal (and impl, barring objections) is ~/.config/sqlite3/sqliterc.

I actually prefer my user binaries to be in ~/.local/bin. That aside, I've went with the wrapper script.

~/.config/sqlite3/sqliterc is the more logical choice, since the CLI binary is named sqlite3 rather than sqlite.

~/.config/sqlite3/sqliterc is the more logical choice, since the CLI binary is named sqlite3 rather than sqlite.

+1