That's right, there are those guys too. I thought they were kinda cool as well...but also weird.
Mwahaha! Look, we are up in the air and you can't get to us! Now let me just attack you up close, without using any fire arms whatsoever, thus erasing the very point of being airborne and unreachable.
Seriously, they don't use guns. If they are gonna fly and gain an advantage from that they would HAVE to use long distance weapons.
I guess SQUARE couldn't be bothered about making all the battle models into field models, so instead used the 'Captain'. to represent them.
It seems to me that the team for the battle models and the "scenario" team did not properly communicate. They could have used the red Shinra soldier/grunt model that is used inside the submarine, but like the case with the inside of the Shinra Rocket the battle team must have been told "Yeah, just add a Shinra enemy here" without specifying which type.
Or maybe the battleVSfield model inconsistency just did not bother them.
EDIT:
However when I think about it more, the "mutant" battle model was among the first that the development team made (looking at beta footage). Interestingly from this earlier footage we also see the red Shinra commanders. Though we never see an actual battle transition in this early footage I think they always intended for commanders to NOT look like their battle models, which are these "mutants" as we are lovingly calling them.
Perhaps this retains back to FFVI, when the art/sprites for the battles could look significantly different from the field sprites. While this was more a question of a difference in detail in FFVI, the mindset that battle models does not have to look like the field sprites/models may be what is the cause here.
AAAAAND I am reading way too much into this.
See here for beta footage:
http://www.unseen64.net/2008/04/11/final-fantasy-7-beta/