Do you actually think Stafleet builds bar modules and plugs them into ships? Having a bridge module makes some sense, the entire bridge can be upgraded in a matter of hours without ripping out the carpet, building new consoles, stuffing isolinear chips into walls etc., they will not do that for a dinky little bar. Find an empty room, carry one or two replicators in, add a few tables and chairs and you're done.
Parts of the ship being empty most likely refers to the possibility of a adding cargo areas, additional sickbays, crew quarters etc. depending in the mission, it's not about changing the interior of a room.