@barklund I understand what you are saying and agree in regards to separation of concerns. I would say that I would think the intent of modifier was to provide some canned classes and an easy way to implement them with exposing contradicting user styling via the style attribute.
I would be interested in why, as far as SoC goes, you think using style="classname" is worse than using modifier="classname"? In my opinion, they are the same thing. Now, I would agree that if the Onsen team implements something for one element, it would be nice for it to be consistent across all the elements.
Having said that, since navigator is their base navigation element (like the carousel), they are consistent in not having modifier.