The obvious alternative is SQLite, and it has many advantages. If you want to do a "zipped list of files", SQLite does that just fine (that's what SQLar is), but it can do so much richer data. Even if you don't want that, it still offers resiliency that "zipped XML" can't match: if your software or computer crashes in the middle of saving your file, it'll almost certainly corrupt it. With SQLite, not an issue: all transactions are atomic, they either happen entirely or not at all.

I don't know what "mature tooling" you're talking about for zipped XML, but I guarantee you it's not going to be better (or more mature) than SQLite and its ecosystem.