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

Before the weird sex stuff, "gimp" was an insulting term for a crippled person. The fact that it's so long out of common use for that purpose that a lot of folks don't realize that is perhaps an argument for not taking it too seriously. On the other hand, disabled folks are certainly among the most oppressed and abused and in ways that aren't well-understood by most folks, so a decent person should be pretty careful about using language that could be demeaning. I dunno. It feels like an archaic term that ought not have any power today, but what do I know?