What do skill boosting affixes affect and what they don't?
The short answer is, skill boosting affixes will boost secondary effects from those runes as well.
For instance, an affix that boosts punish will also boost the damage caused by the fire explosion when blocking (roar rune). And whirlwind skill boost will cause the tornados to do more damage.
The only thing I'm not sure of is whether or not having a skill boosting your hatred spender (such as cluster arrows) will boost the CA being cast by the sentry. I suspect that damage is still tied to your sentry skill, so if you had sentry affix gear it'll boost the damage.