One thing I’ve been experimenting with for a client is layering files and modes, consider the following:
If you add an abstract layer that will fetch values in discrete files for colors, you can actually use Figma modes while having separate files for Brand styleguides (here my brand examples are fruit).
You can even add a cross-mode at the styleguide level, like dark mode or density if you’re working with space variables. The issue is then that Figma doesn’t match variable mode names across files or collections.