The state and the IRS have completely different systems. Certainly one could be accepted faster than the other.
Most of the time, proof that you filed before the deadline is enough, even if the return is not accepted until after the deadline. And if the return is rejected for some reason, you generally have a 5 day grace period to correct the error and resubmit, or mail the return if you can't correct the error.
And lastly, if you are expecting a refund, there is generally no penalty for filing late, because the penalty is a percentage of what you owe. That's true for the IRS and most states, although I did not look up Indiana specifically.
