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Apply custom logic to taxes on checkout?

Ok, I'm probably reaching here, but here is the situation:

Our client applies custom logic that overrides the Tax Code Netsuite places on SOs. That works great from the GUI. Problem is Web Store orders. Now, I have a  Server-Side script there that will modify the actual SO created so that has the right tax code.

But on the Sckout screen, the user sees that taxes as they are applied out-of-the-box, sans scripted override.

Is it possible to override the tax amount displayed to the customer on the checkout page...?

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