Does - magic pen work with singed Dots or his throw back? and if so is it worth getting?
Yes, yes, and yes.
Edit: Only thing mpen doesnt work on is physical skills that only scale with atk damage like pantheon's skills.
Yes it does, however sorc boots arent nearly as useful as merc treads or swiftness on him. Its much more worth it to get a good amount of MPEN from your rune page and a haunting guise.
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