Then why did Chakotay have 40 or so people crammed into that one little raider?
Why, to evacuate them at a moment's notice, of course!
"Caretaker" is a good example of how little it takes to move a thousand people from harm's way. Another is "Blaze of Glory", where Eddington feels a single runabout would be sufficient to evacuate a contingent of DMZ settlers cum Maquis. Not all that unrealistic an idea, considering how in "The Homecoming", sixty people could be carried aboard that 23-meter craft.