You don't need a new application for this, you just need some upgrades to the ZIM generation pipeline. How about sending patches for https://sourceforge.net/p/kiwix/other/ci/master/tree/mwoffliner to generate category-based ZIM files and the like?

Customisation possibilities used to be better here before https://www.mediawiki.org/wiki/Offline_content_generator was deployed on Wikimedia projects, as ZIM files of few hundreds pages were very easy to make on wiki. Help with the OCG component is also appreciated.

Finally, icnremental ZIM updates are an area of ongoing work. You can probably help here as well: https://phabricator.wikimedia.org/T49406#492033

Nemo