Thanks for the details!
I have found a few issues with the configuration. First, certain taxonomy terms were assigned to be returned as products. As I mentioned earlier, the WooCommerce results page does not allow that, so I have disabled those https://i.imgur.com/gaFWpiO.png
I've also noticed, that the index table engine was set to be used, while it was not configured either to index products. I've switched back yet to the regular engine: https://i.imgur.com/mj6zdtM.png
This should have solved the problem for good, as the rest of the configuration is okay. However the WooCommerce results page does not allow override for some reason. It works fine if I choose the regular results page, but not with WooCommerce.
I suspect this is either something in the theme files tempering with the results (as it has an own engine), or a yet unkown bug. Unfortunately I'm not able to re-create the issue on my test servers, so I have no clue yet.
Can you please add temporary FTP details, so I can debug through the override process to see where it fails? I would like to get to the bottom of this.
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