Thank you for sharing your insights!
Right now, I would say that typography and color assets are an alternative to using design tokens for typography and color. I did a deep dive on the differences between color assets and color tokens on the Penpot blog: Penpot deep dive: Color tokens vs asset colors
This is currently how design tokens work. The themes and sets can either be used on components that are published as a library, or used in the design files, or a combination of both. Any changes to the same named tokens and chosen theme in your design file will override those used in the library. You might find the recent hands-on we did on design tokens and design systems useful for showing these more advanced use cases: https://www.youtube.com/watch?v=TmVuRMf5Ojg (You can also find the demo files in this post: Penpot ✕ Tokens Studio Hands-On Demo, Feb 25th - #2 by LauraKalbag
I know the Penpot team are looking at the workflow for using tokens across multiple files and projects.
