Thanks for your informed replies.
If the Calibre "heuristics" solution cannot be adapted, well, what can we do?
As the EPUB3 support is just around the corner, maybe an EPUB3 compliant solution will be available at that time. For me, svg extended support, mathml and endnotes pop-ups are the main reasons for using EPUB3. I have no idea how widely they are supported now by e-ink readers.
In fact, my endnotes work most of the time with Kobo and Koreader but I had to increase
a lot the size of the anchors (margin-left 0.4em + brackets or accolades). I still find many books -mostly EPUB2 - where it's a pita to try to use them.
I do not seem to understand what's the definition of a "useful" plugin. But this would be another topic...