Modding in Freespace works quite differently from many other games, where mods commonly influence separate subsystems and can work independently. While some 'utility' mod exist, most mods are entire campaigns, and will provide new data or modify existing data for almost everything, for a complete package rather than just a subsystem. The usage of a mainhall is dictated by the data of the campaign itself, and usage of a cockpit is dictated by the data of the ships themselves, and since the new mod is coming with its own wholecloth campaigns and ships (typically), you would need to specifically modify their campaign data or their ship data in order for them to work (which would then not carry over to further mods, as you'd need to make these changes with all their data as well)
While, theoretically it's possible for these types of things to be done generically (a mainhall which is used regardless of the campaign, or cockpits which are used regardless of the ship), this is unfortunately not how it works in the engine. Your only option, as far as I know, is to manually make a series of relatively minor changes specific to that mod onto their table files.
