I want to suggest something simple, but effective and more organized interface improvement.
Any ship, that has alternative special module options, like Phoenix , Reaper , Styx , Hyena , Sword S and Karud , should have a special icon displayed on the ship tree, that represents their special modules.
Upon clicking on that module, you are asked, if you want to start accumulating resources for such module. You can also switch both modules directly from the ship tree, or you can access the Store for module parts.
Screenshot example: Phoenix Engineer
you can confirm to switch the special modules directly from the Ship Tree
you can equip a different module directly from the Ship Tree
you can access the Store directly from the Ship Tree
you can access Arthur Cage’s mission directly from the Ship Tree
This is also useful, because players will now know immediately, what ships have special modules that you can switch, buy or farm to obtain them all.