"Specific beats general" is a specific case of a more general principle.
That principle is "every rule has a reason to exist". That is, if you invalidate a rule simply by choosing to read the rules with a certain order of precedence, you should choose a different reading.
For example, in the PHB's example of the principle (p.11):
For example, a general rule states that you can't use a daily power when you charge. But if you have a daily power that says you can use it when you charge, the power's specific rule wins.
The actual rules of the charge are that you have to end it with a melee basic attack or a bull rush, not that "you can't use a daily power". So if you interpreted things such that the basic rules of the charge attack take precedence over a daily power's statement that, say, "when charging, you can use this power in place of a melee basic attack", then that rules text wouldn't have any reason to exist - it would be telling you that there was an option to do something that was ultimately illegal.
Therefore, it's correct to interpret things such that the daily power's special rules text takes priority. It would not take priority, for instance, over the rule that once you use a daily attack power you need to complete an extended rest before you can use it again. You can always use a melee basic attack during a charge, but you can only substitute this daily power for it once per extended rest. Doing it more often than that would invalidate the rule about the frequency of daily attack powers.
The reason that "specific beats general" is the common statement of this principle is that specific rules (the daily attack power's special text) are often written to invalidate general rules (the charge action's restriction on attacks) under certain circumstances. In that case it's not choosing the order of precedence but the rule itself that's causing the invalidation, which is fine.
The hybrid vs. skill power interpretation
The hybrid rule is the invalidating rule here. You can freely select powers from both classes as you level up, but it is not valid to choose or retrain a power that results in you having at least two at-will/encounter/daily attack powers, or two utility powers, but not one from each of your hybrid classes.
This means it should take precedence over the skill power rule, which expands your available selection of utility powers to include non-classed skill powers. In other words, "you can freely select powers from both classes and the non-classed skill power list as you level up, but it is not valid to choose or retrain a power that results in you having at least two at-will/encounter/daily attack powers, or two utility powers, but not one from each of your hybrid classes."
I'd be inclined to make exceptions as a GM, especially in a case like this where the rules lock you out of an option you might be interested in for pretty much an entire tier of play, but they'd be just that: exceptions to the rules read in their proper nesting order.
