I think what made that scene where Kirk called Scotty on Earth from Klingon space offputting for some was that they were doing it with handheld communicators. Many has been the time we've seen on TNG and DS9 Picard, Sisko, or whomever speak with someone from Starfleet Command on their desktop monitors, so it may have seemed less credible that they're using handheld comms devices to make an interstellar phone call than the ship's more powerful communications systems. It's conceivable Kirk had Uhura patch his communicator into the ship's comms systems to speak to Scotty.
Something I've noticed: Abrams has pretty much dismissed intercoms and desktop communications terminals in favor of using the handheld communicators for pretty much all person-to-person communications purposes. Guess it makes sense since eventually the TNG-era shows effused the shipboard intercom system in favor of just using the commbadges for that sort of thing.