Can trillium store all files in markdown/plaintext?

Content is stored in a SQLite db (with options to export to markdown & al.), Trilium is open source, so there's no lock-in and you get the best of both worlds.

How is the theming by trillium? I use a light tan interface because it is much easier on my eyes, personally than high contrast white or eye-straining dark themes.

You can totally reimplement the whole UI if that's your thing, everything (or close-enough) is a note in Trilium, including themes and other JS/CSS notes that will override or extend parts of the application, like add-ons would elsewhere.