All that tends to fit sensible schemas and managing it is what SQLite shines at.
- Continuously parsing and writing and reparsing text, 90% of which is useless (that's the JSON/S-expressions vs XML argument)
- Forcing a diverse relational structure to fit a tree hierarchy, hand-writing all the logic that manages representation change - either explicitly, at serialization boundary, or implicitly, in every single access operation you're doing to refer to some data;
- Or worse, using an off-the-shelf, generic object/XML mapper, in which case you just compound the bloat even more.
SQLite is one of the single most battle-tested and ubiquitous piece of software in the history of mankind. Anything "simpler" you're going to pick up is much more likely to be buggy and broken, and will definitely be orders of magnitude slower.
With a zip file at least you know your file was corrupted.
It's all the metadata around the image that's interesting. Images have layers, dozens or hundreds of them (this literally scales with how good your software is at handling those - the faster, and more powerful layer UX is, the more they get used). Some are pixel layers, other are effect layers, text layers, vector layers. Layers have metadata - names, sizes, colors, tags, types, special effects, and a bunch of other stuff I don't know because I don't use that 80% of features of GIMP/Photoshop/Affinity.
Then you have document level metadata, UI-specific metadata, etc. Also undo history. A lot of that is relevant to the work on images themselves, and changes in realtime, and can get even more useful if querying it wasn't such a PITA.
That - not the binary pixel blobs - is the selling case of using SQLite as application data format.