i had a similar issue, where i wanted to show different subcartegories inside a main category
- shoes
- men
- shoes men
- women
- shoes women
so inside shoes i wanted to show both men and women shoes whilst non of these items should be required to be in category shoes..
your tax_query might be correct but you have to look inside your query for more query variables.
use echo '<pre>', print_r( $query ), '</pre>'; inside your pre_get_posts function.
in my case, the very first entry was [product_cat] => shoes so i wrote unset( $query->query_vars['product_cat'] ); to remove that entry, and that worked on my end.
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