That isn't how phasing works. Speedsters can phase other objects that they touch. When Thawne reaches into Thor's chest he's going to vibrate Thor's heart and then remove it for Thor's body, THEN stop phasing.
Eobard's hand isn't more durable than whatever hyper advanced metal alloy Atom's suit is made of, but he was still able to reach in and remove his heart all the same.
That's all speculation since the only time they successfully harmed someone with phasing it was always a human with no notable durability feats