It is true. If you try to use a transpiled language with JS web frameworks, you may encounter integration problems. That’s why I wouldn’t use JS web frameworks.
Now, I know what you’re going to say. Why should you pass up on all the wonderful JS web frameworks out there? Angular. React. Meteor. Ember. Backbone. Knockout. Polymer. Mithril. The list goes on and on and on and on. These frameworks come and go, having the lifespan of a fruit fly. You get the picture. The JS framework landscape is terribly fragmented, and there’s no sign it will get sorted out any time soon.
I’d rather stick to whatever transpiled language I’ve chosen (e.g., Amber, ClojureScript, Dart, Haxe, etc.) and make the most of that language. Some of them may even have their own upcoming frameworks. I use Amber and I rather like it.
I also use Amber with Cordova to write cross-platform mobile apps.
You can use a transpiled language with most JS libraries and some JS frameworks. You just need to be more selective and cautious with your choices. And, of course, you can always rely on that old standby, jQuery.