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Warmachines and crew seem to be considered separate units, and in some cases have different keywords. When a warmachine shoots, do the crew keywords or the machine keywords matter for determining buffs?

A specific example that I'm thinking about is Queen Khalida's buff, which gives +1 to hit for all skeletons during shooting. Screaming Skull Catapults are not skeletons, but the crew are. Do you get +1 to hit with SSCs or not? It would make sense for the bonus to apply as the crew is the one whose "skill" will matter in firing the machine, but technically the attack belongs to the warmachine's profile and merely checks the number of crew in proximity.

Are there any official rulings on this kind of thing?

I know of this issue and it needs to be FAQ'd in my opinion. I would argue that RAI the buffed crew improves the shot, I think the RAW is open to interpretation.

Notably on every crewed warscroll, it says that in the shooting phase "They [the crew] may shoot the Warmachine", making me think that the Warmachine is fired by the crew like any other missile weapon and buffs applied to them apply to the shot.

It's ambiguous and needs an official ruling.