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Trying to sort what would be a better HQ challenger/clean up crew. Will be riding a Stormraven into battle with a flame assault squad (salamanders) paired with a bunch a drop pod grey-hunters.

Captian Pellas - special rules to mess with HQ choices, ap2 at i5, ws7 + combie flamer.
PF/SS/Artificer cpt - straight forward 2+3++ str8 unit.

Pellas is still a very vulnerable character without a 3++ or EW. So I don't know that I'd call him a HQ challenger, certainly a decent leader though and fluffy.

I actually like the special Apothecary that gives a 4+ FNP, awesome in a Honour Guard squad.

In your situation I'd say the PF captain might be the better choice.