There's ways to rationalize it, but they're all ridiculous.

Every one of those ships had a fleet of fighters on board. Even if you've got a few working aircraft here or there, the only reason Randy Quaid's effort was allowed to happen was because of mob numbers.

Also, we're ignoring that the mothership just allowed in an old ship with no authentication whatsoever, after it just shows up outside for no reason. So this super advanced alien race can't keep track of what ships were lost 50 years ago and, maybe, not simply trust them by default?