I think both statements are valid to some extent.
Storing data (especially, when it comes to application state) in DOM is one problem, attempting to use DOM for meta programming is a different one.
Interestingly, trying to solve the first problem could sometimes result in leaning towards the second one, as we can see it when looking at github.com/google/uniflow-polymer
In my opinion, all these problems have been implied by the two way data binding system and how it affected the way of thinking of Polymer users.
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