The SK only drops yellow on your first kill of him per character.
That is incorrect.The possibility of a boss (or anything, really) dropping magic gear or rare gear when you kill him remains intact on kills subsequent to your first. The probability may change, but it does not change to a probability of zero.

To be clear: On your first kill of a boss in normal difficulty, you are guaranteed a random rare and a class rare, as well as some blues and other stuff. All other kills on all difficulties result in standard drop probabilities. You have a decent chance of getting a rare or two every time you kill a boss.

If they do drop 1/100 later that is probably fine, or better than fine, but why not just make that the "rate" earlier?
I don't know what the drop rates of magic and rare gear from barrels are, but I hope they're way less likely than 1/100.
... because you only need to see that yellow helm flying out of a broken barrel once to change how you see the game forever.