quarkus-qute | using Quarkus with server-side templates | Application Framework library

I would like to write an app that allows for both RESTful forms of interacting with the data; regular REST CRUD endpoints and a web-ui.

In the past, I have gone the route of implementing much of the functionality of the UI in JS, which would call the regular REST endpoints. This worked fine, but for this application I would like to use Qute to perform much of the basic functionalities of generating page content. However, for me to properly manage the endpoints and ensure proper RBAC control, I need jwt's to be accessed via cookie, rather than normal headers. This seems like it is possible, but not at the same time as my other endpoints that need it in header form.. (Source: https://quarkus.io/guides/security-jwt#microprofile-jwt-configuration )

What might be the best practice here as well? Should I just keep the two apps very separate, and do everything in Javascript?

For reference, on how I am using jwt in code: (example from UI qute generation, but I am using the JWT in the same way for CRUD endpoints)