It seems that the Checkout API is able to both create customers and take in a customerID so as to not make a duplicate customer.
Is it possible to save a payment method to a customer via Checkout API?
Currently, with the Cards API you can save a card on file with the payment_id from a payment that was completed with the Checkout API. 
Awesome!! Will these cards give the option to autocomplete the payment info in a checkout page where a valid customer id is provided?
I’m not sure I follow. Once a card is saved on file you’ll need to use the Payments API to complete any future payment. When you get a chance could you share more on what you mean by autocompleting a payment in a checkout?
A little context: I’m writing in an Expo managed React Native project. The use of the In App Payments SDK requires me to eject from Expo as it is a purely native package. The only way I have found to generate a card nonce is using the In App Payments using SQIPCardEntry.startCardEntryFlow; however, I have found that the Checkout API simply redirects the user to a webflow and the app is not required to generate the card nonce.
In my question, I am referring to the webview that is generated by the Checkout API. As far as I know, this is separate from the Payments API, correct?
This all stems from me not being able to use the SQIPCardEntry.startCardEntryFlow portion of the SDK in our Expo React Native project. I tried to eject from Expo and we had other non Square related issues with our android vs ios build blah blah, don’t need to get into that.
Another question (this could probably be a new thread): The SQIPCardEntry.startCardEntryFlow popup module seems to be the only way to genereate a card nonce. Is there any other way to generate a card nonce?
Thanks for further explaining. Yes, the Checkout API is separate from the Payments API. Also at this time the only way to generate a nonce it with In-App Payments SDK or the Web Payments SDK.