I mentioned this before in one of these threads, but I think we're supposed to pretend that the Beyond Enterprise is how the ship looked at the end of STID when she headed out on the five-year mission.I hadn't noticed the extra phaser banks on the saucer. That seems to confirm that there's no way that the new Lin design from the beginning of Beyond could be the same as the repaired Enterprise from the very end of Into Darkness (not that I thought it was). Again (assuming these photos are accurate), that would imply that sometime during their mission, in between those two movies, they would've refitted the saucer with double the phaser banks, enlarged and added windows around the rim, and completely replaced the neck, pylons, and nacelles.
With the ease that the designers can tweak these models now, it seems like we have to accept that major reconfigurations like these are fairly standard.
Similar to how in Search for Spock she had five times as much battle-damage as actually suffered in TWOK.