No, the message your "Your Federal return was accepted." means exactly what it says. You submitted your tax return by e-file and the IRS has accepted your tax return.
E-file acceptance is a basic computer matching of data like names, dates of birth, Social Security numbers, and a few other items. Additional matching and screenings will occur later in the year.
Since you say your bank has confirmed that your tax payment was made, you can assume that it was, and that you won't be penalized for late payment.
The fact that the IRS accepted your payment doesn't mean that they agree your tax return is correct in all respects.
None of this has anything to do with audit risk. All tax returns have some audit risk, but for most taxpayers the risk is low.
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