That doesn’t mean what you think it means. The “yes” in that column means that the variations post type is set to be excluded from search when it’s created, but it doesn’t mean Relevanssi can’t index it.
If you check the box, Relevanssi will index the product variations. Because it is set to be excluded from the search, you then have to uncheck the “Respect exclude_from_search for custom post types” setting on the Searching tab of Relevanssi settings, otherwise Relevanssi will see that the post type shouldn’t be searched and won’t search it – but once you uncheck that option, Relevanssi won’t care about what WooCommerce wants and will search it anyway.
That said, it’s often a better idea to index the variation SKUs for the main product, because there’s a reason WooCommerce doesn’t want you to search for product variations (for starters, many WooCommerce themes simply don’t include anything but products in the searches). Here’s how you can do that: https://www.relevanssi.com/knowledge-base/indexing-product-variation-skus-main-product/
