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Pending Payment E-mail option is there to allow you to send your email notifications and autoresponders even if the payment was not made.
In a way, yes, it means that you could send an email stating to the person that submitted your form that their submission is received and that payment is pending, but this is sent right after they submit the form, not later - to remind them.
It also means that you would be able to set up your form to let you know once someone submits the form even if they did not pay, and since you get their details - such as email on the form, you could simply follow up if they do not pay you after some reasonable time.