If the taxes have been paid, I don't think there are bad consequences if the filing is accepted. If the filing is rejected, then it will be after the grace period for re-transmission and I think you have to mail in the return with the corrections, along with arguments of why it should not be considered a late filing, which NJ could accept or reject. In my case, I would use the confirmation code for the extension.
I don't know about the case where the direct deposit instructions are contained in the filing as to whether that would be considered timely or late.
