I would rule No. You aren't making an attack roll, and thus no effects that come from making an attack roll can be applied. It's the same reason why spells that are defended by saving throws cannot roll critical hits but ranged spell attack rolls can. That's my basic thought on the game rules portion of the question.
By the fluff part of the Seeking Arrow ability... the Fighter isn't actually aiming his bow and firing (which is what normally allow him to choose to take a more difficult shot at an important body part for the extra +10 damage.) Instead, he just fires randomly and the arrow flies on its own towards the enemy... going around corners, flying through cover... to reach the target, and the target has to dodge the arrow to take less damage (via a Dexterity saving throw.) If you aren't aiming your arrow at a deadlier spot on the body, there's no way to get extra damage from it.
And finally... there's just "What does common sense tell us?" And common sense tells us that by your reasoning a person can just add 10 point of damage to every attack they make with Seeking Arrow with absolutely no penalty if they have that feat. And we then ask "Do we really think that's what the game intended to have happen?" And most likely most of us would respond "No. The game would not expect someone to gain 10 free points of damage on an attack with a single feat without penalty."
If you want to give that player 10 free damage on two Arcane Arrow shots just because... you're more than welcome to obviously. But to me this is one of those "If it seems too good to be true, it probably is" situations, and besides which, my first paragraph went over how the rules themselves really don't support the idea either.