Hi Michael,
As promised, we’ve released new plugin version 1.4.4 today. After the update, you will find new “Query post type” option in each feed’s settings (in “WooCommerce > Settings > Product XML Feeds > XML Feed #X > Advanced Options”). Please set it to “Products only” – this should solve the issue with variations filtering by product’s category.
The reason why we have added this as an option (and didn’t just make it the default behavior) is that in this case XML creation is a little bit slower (as we need to check every variation of a variable product manually). Anyway please try it out, the difference in time should be minimal.
Please let me know if something is not working as expected. And if you like the plugin, please consider leaving us a rating.