I just realized that every shipping module I've looked at includes a couple of configuration settings for their shipping-tax calculations: a Tax Class and a Tax Basis.

Those values are loaded into the shipping-module's class variables on initialization and, when a quote is requested every module I've inspected has the exact same block of code to calculate its tax-rate:
Code:
    if ($this->tax_class > 0) {
      $this->quotes['tax'] = zen_get_tax_rate($this->tax_class, $order->delivery['country']['id'], $order->delivery['zone_id']);
    }
Yup, using the country/zone from the Shipping address for the calculation and totally ignoring the other Tax Basis settings. I'm just pointing out the anomaly: Either the tax-basis should be used in the calculation or the tax-basis setting should be removed.