PayPal MC duplicate payment: Refund process not intuitive!

I made a manual payment for the full statement balance (over $10K) one day before my Auto-Pay happens because I changed my bank and I was worried Auto-Pay would have some trouble. It turns out Auto-Pay made another payment of the same amount, thereby leading to a double payment.

When I requested a refund for the duplicate payment, the customer service stated that:

• The duplicate payment has to sit for 7 days before they can send me a refund check.
• After they send the refund check, it's another 7 to 15 days for the mail to reach me.

In total, the refund takes up to three weeks or more. Overall, it is odd and not reassuring that:

1. It takes so long for me to receive a refund. It shouldn't take more than one week in my opinion!
2. A mailed paper check worth over $10K is the only way I could receive a refund. This seems risky. An electronic refund would be faster, more convenient, and much safer!
3. The Auto-Pay made a duplicate payment. It seems easy to write software that prevents Auto-Pay from making a duplicate payment!

Do you know why PayPal Cashback MasterCard behaves in these non-intuitive ways? Are all these behaviors just standard in the credit card payment world?

Thank you in advance for your feedback!