I think one could use a requirement system for the tower creation. Similar to Space Empires series ship creation, the ships have minimum needs that take space and needs to be fulfilled. A layered grid should be sufficient for a tower. (Imagine houses. Grids are rooms and layers are floors.)
Say a tower needs power supply/intake, a targeting system, rotation engine.
To create a tower, the player must add these required items to complete the creation process. They could easily also have different types. f.ex. one targeting system could be able to aquire targets faster, but would sacrifice range to accomplish it, while another targeting system could do it the other way around.
After the necessary requirements are fulfilled, the player could then proceed to add other items such as armor, weapons, passive stuff, shields.
A method like this is fairly simple and allows for extremely large number of different towers.