Yes, the tax status will affect things.

For example, let's say the item has a tax status of 2 meaning that it is GST & PSTable (let's ignore HST for the moment please) and the customer has a tax status of 1 meaning that it is GST taxable only. When the item is receipted as an invoice, the lower of the two tax statuses (eg. '1') will be selected by the program. This will be the tax that you see on the receipt invoice Totals tab and that will be sent to the appropriate GL account. Remember, the GL account is defined when you select the jurisdiction costing method of AP in the Tax Group.