Why does it want to charge 39.99 to deduct from my federal but then says it wants to deduct another 39.99 as option to pay with refund resulting in being charged twice?

You are posting from Deluxe, which costs $39.99; if you choose the refund processing in order to have that TT fee deducted from your refund, there is an EXTRA fee--also $39.99-- in order to do that.  It is cheaper to pay TT upfront with a credit card.

And if you prepared a state return using online Deluxe, the state return is another $39.99.

or   Maybe $40 for the state forms and $40  for the option to pay with the refund.

$40 Deluxe, $40 state, $40 option to pay with Fed refund  (…the final option...which many of us try to talk people out of doing.  Just pay with a credit card.