Since ATS appears to create its categories on the default Joomla category manager, Seblod intercepts the call (as it does whenever a new Joomla content category is created).
The resulting category is saved in the Joomla category manager, but ATS does not see it.
In the modal prompt launched by Seblod to pick a category handler, there is a Standard Joomla option, although it still leads to the Seblod Category content type, instead of Joomla's category manager.