Is the amount paid for FREE Cancellation, Paytm Service Charges and Payment Gateway Charges also refunded when I cancel the train ticket within the free cancellation window

No. The amount paid for FREE Cancellation, Paytm Service Charges, Payment Gateway Charges are not refunded even if you cancel within the free window. You, however do not have to bear any cancellation charges from Indian Railways & IRCTC during the free cancellation window.