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And HR is going to give a contract (via agency) employee the time of day why?

Because that's pretty much their job.

Even if his paycheck is through the agency, the agency contracts him out to Apple and he's just sitting there at their desk?

He's describing a harassment problem with his boss, an Apple employee, pretty sure Apple HR is the point of contact for this scenario.

Let's suppose he was being sexually harassed by his boss--do you think he'd go to the agency to resolve this?

Right, that is complete fantasy. Everybody involved held a better hand than this guy, and he made the right decision - choose a different game.