A thought if you're looking for an in-universe/story excuse for this kind of thing: the photonics rebelling against the Hirogen after Voyager gave them holodeck tech. Heck, they were building entire ships that consisted of nothing but engines, a computer, sensors and holo-projectors. And then shooting Hirogen with holographic phasers with the safeties off.
You could use that excuse for why we'd get ships out of the lockboxes. Include the flicker effect on them, and underneath it's just this small ship with a small bridge, projecting out the holo-Captain Proton ship or whatever.