I've not used xquery enough to know if it can be succinct enough to be used as jq's language can.
For sure the Saxon cli could be made a lot more user friendly if it followed normal conventions.
But now it doesn't matter because the backing format doesn't really matter and JSON was there at the right place right time.
Find me a programming language where objects have attributes, the order of members is significant and can be interleaved, everything is stringly typed etc...
It's a shame because I agree the tooling for XML is still better than JSON. But not better enough that it's worth fighting the data model mismatch.
Though, personally, I prefer JSON. Probably due to superior tools (thanks to its popularity) and less-bloated syntax (it is somewhat easier for me to read raw JSON file than raw XML file).
When XSLT 3.0 tells a joke, it starts with "a JSON walks into a bar..."
FWIW https://saxonica.plan.io/projects/saxonmirrorhe/repository seems to be the for-real source repo
Now compare this with JSON ecosystem
Saxonica, the company behind it, has been critical for the evolution of the XML ecosystem.
I agree that lack of alternatives sucks but the breadth of options you refer to is backed by an army of open source volunteers.
It would be cool to be able to use XPath to query JSON. Of course you'd need to come up with a good mapping between JSON nodes and XML nodes.