It was essentially confirmed in the Journal that Valeriana is a ghost of the newt who invented the music box and has been wandering the mortal plane out of guilt and wanting her mistake undone.

And "overarching" means they are protagonists who have more contribution, scope, weight, etc. than the main protagonists. I can see that for Leif, the Guardian, and Valeriana, but not so much Sasha I admit.

To qualify, I think they have to have central contributions with less screen time than the main ones.

A protagonist is defined not by their scope, weight, or contribution to the show's lore and plot, it's about the show's theme and overall focus. They are overarching characters sure, but most definitely not protagonists. Valeriana creating the music box and being a ghost should be cited to avoid confusion, and with information as big as that, why has it not been mentioned on the journal's page?

Probably because the information comes from the runic passages.

And why they not protagonists at all, even the ones with the official heel-face turns?

Wut