I appreciate when someone takes time and effort to dig into an issue; I would answer some of your doubts here, but I would prefer to continue the discussion on GitHub so we can land at the end with a fix and a new release.
please open a pull request and I would ask @rodfersou to help you.
"legacy" in the new Plone 5 resource registry terminology means JS and CSS resources that are loaded using an older approach: in Plone versions < 5 there were the portal_css and portal_javascript utilities; you registered your static resources there using a simple XML file that you can see here:
that was good enough in the old days, but showed its limitations as soon as client side code became more and more popular.
the new resource registries use a different approach and tries to bundle everything at runtime; that's IMO the chief problem: instead of keeping the old machinery and deprecate it gradually, core developers decided to replace the whole thing with something new and more complicated that is not playing well with old-style add-ons.
on a related topic, we have developed a completely new approach of bundling resources in our add-ons using webpack and we are pretty happy with it.
I think the first thing we need to do is update collective.glossary resources to use this approach; then it would be easier to fix and maintain it.