Why after already paying the state taxes due is TurboTax confirming a federal refund that is less the state tax payment that I already made?

At the end Turbo Tax shows you a summary of the net combined federal and state.   But that is only for your info.  You will still get the full amount and need to pay any tax due separately yourself.

Turbo Tax isn't updated after you file or pay.  Turbo Tax doesn't know if or when you paid.  Your return will always show the tax due.  

You might be getting confused by the summary shown in TT that nets out the difference between your federal refund and the state tax you owed.  It is not possible to pay your state tax from a federal refund, so you do not have to worry that that will happen.   TurboTax never, in fact, knows when, how or even if you paid your tax due.   TurboTax only displays the result of the tax returns you prepared using its software.