the SQLite archive format (it's probably worth linking to the main documentation[1], instead of the very old experimental repository) may not really be a good fit for something like GIMP's native file format. (To be clear, "SQLite archives" are not special compared to any other database: it's just a well-defined schema for an sqlar table, which the sqlite3 command line tool is able to create, update, and extract using syntax like the tar command.)

That being said, SQLite would still be a good choice, especially as it's a format that's really intended to be modified in-place, and has good data integrity features (eg: keep WAL enabled so that mid-save crashes/shutdowns don't corrupt your file), neither of which are provided by Zip. You could even just run zlib on data (be it XML or what have you) if optimizing the on-disk size of the file is desirable.

[1] https://sqlite.org/cli.html#sqlite_archive_support