Perhaps add a command to Constructors...go to closest Starbase that has available modules. Then allow you to designate modules as undesired for building for both specific starbases and globally. Of course this designation would not be permenant. And specific always over rules global. I imagine under the civ manager a page for managing ships, and part of that page would be for Starbases and constructors...
On that page, would have a tab were it would list all possible (based on technologies) modules, each would have a check box next to it...if the check box is unchecked then the module is considered undesired and not considered for construction when auto sending a constructor.
Also on that page, on another tab would be a list of all the starbases and a list of all the constructors...the constructors would have their destiation (waypoint, resource, starbase, or empty space)...from there if you click on a starbase: A number appears next to each constructor, which is the distance between the constructor and the starbase. Second data on the starbase is shown, so you know which modules are built, where the starbase is, what modules are available to be built, and bonuses the starbase grants...
From the starbase information you can get a list to specify for that specific starbase which modules are undesirable for that specific starbase.
Interesting part comes when you get new modules and want to change the global settings (do they change the old starbases that previously couldn't build...)?