Yes, once the customer confirms Via pop up they will still get an sms otp following your template. We added this because some customers tend to close the tab as soon as they order. So they will still get the SMS link to go to the OTP page and confirm their order.
Now, assuming the customer already confirmed their order on the OTP pop up. The link will lead them to a thank you page telling them that their order is confirmed. You can customize this page too.