Im paying for the TurboTax plus package, unfortunately I cant get a clear answer to my question. Does the $40 refund processing fee apply to those who owe $??

No.  Only if you are receiving a Federal Tax Refund can the $40 refund processing charge be applied.

No.  That is only if you want to have the fees deducted from a federal refund. If you have a tax due you don't have a refund and it wouldn't even offer you the 39.99 Refund Processing Service.  Or do you have a federal refund and owe state?