So what happens with all those JQuery plugins that manipulate the DOM directly in didInsertElement?
I'm guessing Glimmer doesn't have a clue how to optimize that use case. So a lot of components need to be rewritten from scratch in Ember-style?
Well, if you need the performance increase, the yes. Otherwise your options are to (maybe) tweak your current implementation so it continues to work or rewrite the functionality to be compatible with the view layer. This is the same trade-off you make with React since it's basically the same technology.
You shouldn't be both manually manipulating the DOM _and_ using Handlebars mustaches for the same element. Since there wouldn't be mustaches, Glimmer would ignore these cases. In general, you should only be using jQuery plugins for special cases not covered by Ember anyway.