I agree with you, as far as the dual layers of communication. The general feeling I get is that that's precisely why Pixar is a preferred studio over some of their competitors in the animation space.

I didn't see Onward, but between that, Coco, Soul, and Inside Out, those are four moves that grapple pretty heavily with mortality, death, the afterlife, depression, which I'm assuming sails over the head of most kids.

And even their earlier ones like Finding Nemo, Ratatouille, and Up have pretty serious things to say about childhood illness/"deformity", the role of the critic, and tragedy that similarly seem to be aimed -just- over the heads of kids.

I think I'd need a definition of what a "great" childhood story is, but I'm pretty sure that neither Disney nor Pixar has "controversial" as part of their DNA. Much to the relief of parents everywhere, that's simply not what they're trying to do, so to judge them for not doing that is confusing.

Perhaps you're looking for something more along the lines of A24 (Moonlight, The Florida Project, The Witch) from... Disney?