Sorry for the delay, I didn’t receive the notification for your post.
This is not possible now, but I am currently developing a new Per-Level Product Rates feature for the WooCommerce integration (More coming soon). And that feature will enable you to set a Per-Product Rate of 100% (Direct) and a Per-Level Rate of 0 on all levels for that product. This is estimated for release by the end of the month.
It would still require a quick code snippet to ensure that the 0 amount applies.
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