That Ridley fight would have been incredible and it explains the concept art a lot more

i wonder if the meta ridley fight in smash bros brawl was a callback to this unused idea...?

I think if they wanted to have a Ridley fight like the one described I think they could have gotten away with it by just having a separate world area that the fight takes place in, and there are scan points that when scanned, the ship automatically reacts. Basically Prime 3 when you would tell the ship to blow up walls or pick up objects, but confined to a boss fight.