Yes - anyone who subscribes to the List that is connected to your Welcome Series will enter the Flow. This includes customers who subscribe during the checkout process in Shopify (prior to May 25, 2021, customers who subscribed at checkout in Shopify did not enter the Welcome Series).
During the Shopify checkout process, your customers have the option to subscribe to your main marketing List:
If they check the box to accept marketing, they will enroll in your List after they successfully complete their order. Once they are in the List, they will enter your Welcome Series Flow. Please note that if your List has Double Opt-In enabled, the customer must confirm their subscription in order to enter your List and enroll in the Welcome Series.