I have set documents with 500 or 600 pages and a lot of chapters (mostly with a separat story for each chapter) in one InDesign document without any problems.

What is the reason for having 12 endnotes instead of one? There you could put the content of each of the 12 former endnote into a separate paragraph.

I don’t know what the Script does. But otherwise I could only think of a lot of manual work. And it would require to change the footnotes to endnotes. So you can place the foot- respective endnotes in separate text frames and apply text wrap wherever you need it.

Not 20 years, but 12 years or less are somoe Articles about Accessibility in InDesign Magazin: https://indesignsecrets.com/indesign-magazine-topic-index

“but if the master pages have text frames. ID seems to treat my seperate articles as one long story.”
I think that’s how InDesign is supposed to work. I had the same issue some time ago but could not find a solution. So I ended up working without primary text frames for this project.

If you export the tables as pdf file, you can place a table, then duplicate and move it to another page and make the frames smaller, so that every frame is just showing the columns you need. You can edit the original document (it can be the same document with the tables on a hidden layer or outside of the page), export as pdf again and InDesign let’s you update the placed pdfs.