I know this post is rather old now, but I agree with much of what you have said. However from what I can make out, one of your issues can be fixed in the current 2018 version. In the Type menu there is a Document Endnotes Options section. In the following dialogue box there is a dropdown button that allows you to change numbering from continuous to per story.
I know this post is rather old now, but I agree with much of what you have said. However from what I can make out, one of your issues can be fixed in the current 2018 version. In the Type menu there is a Document Endnotes Options section. In the following dialogue box there is a dropdown button that allows you to change numbering from continuous to per story.