I suspect (though I don't remember for sure) that you'd have to overlook Main Engineering changing back to its 2009 incarnation after the events of Into Darkness, though.
They did use the same brewery for some of the Engineering scenes in STID. They just added location shooting at Livermore Labs for the actual warp core (as well as for a loading platform in the hangar bay, apparently).
Anyway, the comics are full of art-reference errors -- the wrong version of the Enterprise
or the wrong phaser design or what-have-you -- so it's best not to take the visuals too literally. Which is a habit that fans of DC's first TOS series also had to learn, since its artists had a very idiosyncratic way of drawing the ship interiors.