I got it to work (thanks to ACF support), so it seems only right to let you guys know if you ever run into this problem.
The solution for getting the repeater values to appear on the WooCommerce search page was the use of acf-json. This way, the field groups are loaded locally and not from the database. So the field definition lookup query is not affected by any other WP filters.
Worked like a charm!
Welcome to the Advanced Custom Fields community forum.
Browse through ideas, snippets of code, questions and answers between fellow ACF users