Something I've started doing in my workflow is using Pandoc to convert between Markdown and DOCX when authoring long documents. This lets me put the Markdown into Git and apply the Gemini CLI to it. When referencing other documents, I'll also convert them to MD and drop them into a folder so I can tell the AI to read them and cross-reference things.

At the start of the project the Markdown is authoritative, and the DOCX is just for previewing the styling. (Pandoc can insert the text into a layout template with place holders.)

Towards the end of a project I'll start treating the DOCX as authoritative but continue generating Markdown from it, so I can run the AI over it as a final proof-read or whatever.

This is similar to what people used to do with DocBook, but with a more friendly text format and a more AI-friendly "modern" workflow with Git, etc...