Yes - you get the free bag if you a card holder at the time of travel. That means you can pay with travel funds (including the deposited Cost certs) or even another credit card. My wife and I (both card holders) have used both the Costco Certs and flights booked via Amex (when they have had Amex offers for AS) and received the free bag benefit.
https://www.alaskaair.com/content/mi...UuwWm_7z6MR8Vc