Just what I need – only with more products

Yes, it can also handle variations as long as they have unique SKUs from the parent product.

You can add support for 5000 (or more) products with this snippet: https://gist.github.com/laurikar/c7603e4013247991fdd12ab7f7e3f2a9. You can add it to your theme’s functions.php file or with Code Snippets.

Please note that the report page (WooCommerce > Stock Sync) may become slow by increasing the limit. I will improve the functionality soon.