This isn’t an issue and the system should finally be changed to allow anything to be in a ship’s cargo bay when it’s put into a ship maintenance bay. An unpackaged Iteron V is 275,000m3 in volume and it can only be pushed to carry a bit more than 42,000m3 of cargo. The only concern I can see here is that you’re arguing how a ship shouldn’t be used as a kind of cargo container for general cargo while being inside the ship maintenance bay … but the restriction on what to put in the Iteron is completely arbitrary. Clearly, the Iteron would fit in the maintenance bay no matter what’s inside of it.
Being worried about using this as some kind of exploit is an overreaction. The game doesn’t allow accessing cargo bays of ships stored in a ship maintenance bay so you can’t use the “bonus cargo bays” unless you unload those industrials and fill them while they’re outside of the ship maintenance bay first. It’s too much of a process to be useful compared to just having a freighter. Granted, there would be a few edge cases where people use this as a creative solution under particular circumstances to move a little more cargo than usual, but that’s fine because they’re spending a bunch of extra steps manually loading everything for only a moderate gain in how much stuff they can move when they don’t have the proper ship to do what they want in the first place.
Even a Bowhead would only get you an extra ~305,000m3 in cargo if you cram it full of Iteron V’s. There’s no point in doing it that way, and people should be allowed to be creative with weird situational needs in exchange for not being a huge hassle to those of us who use use ship maintenance bays legitimately when we don’t want to have to shift things we carry for normal use in our everyday ships.