ZE gunturrets are not affected by the physical projectile damage upgrades
normal turrets are affected twice by each damage upgrade
(once for the turret, once for the bullets)
the ZE turrets are only affected once, this means that by the time you are at damage 6 the basic turrets do more damage then the turret mk 2
flamethrowers have the same issue (not lasers though)
i can provide more info here or over discord (JDs channel -@DeadlyKitten or by DMs), which ever you prefer