Regarding the final output, the total solution is already there. There are very sophisticated pagination programs that handle all the output. And there are many people here that know how to use them very well. But they are not programs that are for writers and content creators. They all work on codes.
The problem is for the content creator who needs the flexibility of a good word processor to create his content keep all notes separately and then deliver it to the the DTP expert.

If you want to see what I am talking about take a look at this. There is one main text in the middle and at least 10 (!!!) sets of "commentaries" i.e notes:

How they did this in the old days by hand is nothing less than a miracle

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