Hey @evanatonecare!
As you mentioned, Retool currently doesn't support including scripts as part of a custom auth flow, though it is a known request and being tracked here. We also have a separate existing internal request for a Cloudinary integration and if that gets picked up we can let you know here as well!
At the moment, the solution we have for running auth that requires scripting is to do so in the app itself so that you can make use of JS queries or preloaded JS. You can also store values in localStorage. So, conceivably, you could have your users log in through a dedicated app that stores the signed token in localStorage, and then reference that in subsequent queries made in other apps.