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My only thought would be that the cannon needs to be away from the main body of the ship because of heat or EM discharge when firing. Of course attaching it to a hand would make that pretty moot :P.
Maybe it's due to energy usage, while in "roid" mode the energy that's used for engine thrust is diverted to the cannon. But then that could be counter by saying, "why would they need to be in roid mode for that".
Ok here's one that actually makes some sense. Having the cannon attached to an arm makes it easier to move in position for target acquisition. Basically, instead of having to maneuver the whole bulk of the ship each time they need to readjust aim, it's the lesser mass of the cannon and arm.
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