I did something like this with a dropship design a while back. It could be converted from a lightly armed cargo carrier to an assault dropship. The limitation was that there were only the 2 configurations- for example a medium laser could be swapped for a large laser but that was it, you could not put in a PPC or an LRM.
Maybe the way to handle Omni-Warships is to base it on turrets. For example you have a turret with 4 Heavy NPPCs that can be replaced with 3 NAC/30s & ammo. I would make crew quarters and heatsinks part of the base design, if the max heat configuration needs 5000 heatsinks, they are put in when the ship is design, so that some configurations have excess heat dissipation capacity. The same for crew quarters.
By using turrets reconfiguration should be fairly simply- you can use a Model 96 or 97 dropship to remove the turrets and replace them and a large cargo vessel to carry the replacement pods.