Kind of. It's the same in
Star Trek (2009) and
Into Darkness up until it gets badly damaged by the
Vengeance. At the end we see it after extensive repairs and it has some differences (much larger impulse engines, slightly different nacelle fins, possibly additional phaser turrets):
Apparently it had further refit work between
Into Darkness and
Beyond because it then changes significantly between those films. The neck is made much skinnier; the nacelle pylons are swept back; and the nacelles themselves are physically smaller. This picture of the Eaglemoss models shows the differences quite well.
My headcanon is that we might assume the refit we see at the end of
Into Darkness is
supposed to be the
Enterprise as we see her in
Beyond. We only get a glimpse anyway so it's easy to write off any discrepancies.