Using Product variations as product addons

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Discussions on WooCommerce is off-topic here, but can’t resist myself answering. I faced a similar issue couple of months back and my solution was something like this.

  1. Remove the default add to cart form and variation choices in single variable product page. You can use JS or modify the template.

  2. Add custom form with checkboxes and quantity input for each variation

  3. Add those checked variations programmatically using woocommerce_add_to_cart hook.