I'm not sure what you're doing if you are seeing that, but when the vendor is set up for use tax, and it shows in the bottom of the invoice, it will not go to job costs as it is included in your sales tax payable account

To have the billing hit the job and the sales tax not show up on the wip report, enter the income on the line with the job number.  On the next line leave the job number blank and enter the sales tax amount.

Sage doesn't offer job #'s in the line items of any of our billing screens.

Are you referring to Sage 300 and not 100 Contractor?  You called it a billing mod.  Sage 100 Contractor has several billing menus: standard (3-2) T&M (3-10), Progress Billing (3-7) , etc.