Well, the simultaneous rules should not apply as the card has a explicit cause then effect syntax, that is not in the simultaneous rule.
Gunner happens independently of cause and effect to, so you always can take gunner simply after you perform an attack with the shuttle. This of course is a prereq. to vader and gunner. However, the Vader wording is not 'instantaneous' as gunner but requires a cause and effect time component- one thing must happen before the other.
The point is that both cases give examples of longer windows than just in Vader's ability, and the ship removal (and end game check) wait for them to complete. It doesn't matter why the order is what it is, it being a cause/effect syntax (which has no explicit meaning in X-wing anyway, as near as we can tell) may affect the order, but it doesn't change how the effects resolve. Or to look at it another way, it doesn't matter if things must happen in a given order, just that they do.