You do have to consider that this all just happened because Vettel was handed a huge tyre advantage. Mercedes had a decent advantage overall over one lap, over the race distance they were anyway never outright quicker except of Silverstone, so Ferrari being close is something which is probably not worrying for them at all in context of the season so far.
Those who believe that either team will have a walkover from now are extremely naive. Singapore will be a outright Ferrari track most likely, Monza perhaps for Mercedes. Everything else might well depend on form.
As for the engine advantage saving Hamilton: He contributed a lot to it himself by lifting early, otherwise Vettel would have got him like the others got Bottas. Mercedes might have thanks to their upgrade a engine advantage now (or at least a topspeed advantage thanks to set-up) but it's getting extremely exagerated. Hamilton build up the buffer in the final stint mostly in the 2nd sector, where the engine has little impact