My perspective on mundane extraordinary abilities is quite simple.
If the Ranger casts hunter's mark, it is an explicitly magical ability that is functionally identical to other spells. The effect can be dispelled, the casting can be interrupted, etc. etc. The Ranger has learned how to cast magic--you can't just hand-wave it as extraordinary skill because mechanically it is not.
If the Ranger has a class ability with benefits similar to hunter's mark, then the class is free to define it as a non-magical, skill-based, ability. It can"t be dispelled, and it doesn't interact with any other ability that affects or restricts magic.
I would prefer D&D to have MORE options for extraordinary mundane characters, not fewer.
I would prefer D&D to have MORE variety in the way class powers are constructed and balanced, not fewer.
I don't think forcing abilities into the spell system makes them any easier or harder to balance against other abilities.
Making most class abilities default to their equivalent spell, and giving most classes spell slots, sacrifices interesting play, immersion, and campaign options for the sake of mechanical 'simplicity', as if WotC are terrified of having players learn new rules for new classes.
I'm quite happy with mundane abilities being limited use, X/day or X/encounter, or drawing from a pool like the battlemaster. I am very frustrated with the tendency to grant almost every class spells by default.