Yeah, they'll probably have to change a few things to make them more consistent.
Like I said Alch Stun and Dagger and mystic Snake on stone targets should all work the same, can't target a Spell Immune unit, but can damage them if Immunity was activated after the projectile was "fired" (or make them all not damage).
The main issue, however, is with AoE spells. Like, with the current wording Crush can't damage Spell Immune targets if Timbersaw abilities are not allowed to.
They should add a part about all Physical AoE spells then and make it clear that the damage will alway go through, because we may know it (or rather, we did, because things have changed, but if they stay this way we'll get to know them anyway), but it's still kinda obtuse.
Like you said earlier, it's weird that Echo Stomp would work and not Crush. Maybe just an oversight. I checked if it was on dota2dev; if it is I'm not seeing it. Poor Slar.