As for markdown, great. Now how do you encode the meta data about the confidence of the model that the text says what it thinks it says? Becuase xml has this lovely thing called attributes that let's you keep a provenance record without a second database that's also readable by the llm.
If you already have a high optimized pipeline built yesterday, then sure keep using it.
But if you start dealing with PDF today, just use Gemini. Use the most human readable formats you can find because we know AI will be optimized on understanding that. Don't even think about "stitching XML files" blahblah.