Great work, kudos! I am working in a project that makes extensive use of webcomponents. Fancytree works quite well in polyfilled shadow DOM, but with native shadow DOM, features making use of jQueryUI break. I have switched from 'dnd' extension to 'dnd5' extension, which got me DnD working in a tree in shadow DOM.
Webcomponents, especially shadow DOM, nicely confine things inside a DOM tree branch. Libraries working from a node downwards usually work fine. The traditional jQuery/jQueryUI based libraries, however, pose integration problems. jQueryUI breaks because of event retargeting, jQuery selectors are not able to cross shadom DOM barriers.
Are you still heavily relying on jQuery and jQueryUI in your development? Or are you phasing them out?