At the moment this is not possible. The filters work only on categories and immediate subcategories.
We would consider enhancing the filters to work for more than two levels of categories for the next version. However right now we have two really strong arguments against this:
1. We believe that more than two level of categories for an e-commerce website is not very user friendly and most e-shops try to avoid this. In fact you will rarely see such an organization. However in your case you have your top most category hidden. So I am wondering why this is?
2. The performance implications of having all the products from a category tree to be filtered are enormous. So if we are to implement this it would really have to be well thought of and worth the effort.
Our shop has more than 2 level categories and we are currently using version 3.4. In your ajax filter plugin, it is not showing properly if category levels are more than 2. Like in our shop we have a category like White wine >> Chardonnay & Blends >> Chardonnay. All products are mapped with Chardonnay. When we browse White wine ajax filters are not available. Can you please explain why this is happening?
We answered you on the ticket. Most probably you haven't enabled the "catalogsettings.showproductsfromsubcategories" setting and this is why you don't see the filters in the parent categories.
Hope this helps!