Hi. How you setup weapon swap in your project is really up to you and how you decide to code it. In the character creator it's simply a unique game object for each weapon that gets shown and hidden when you swap. I have no experience with gadot so I don't know if there is a better way of doing it.
Viewing post in Character Creator 2D - Modern comments
You can try this. Export your characters layer by layer with only 1 layer visible (only 1 piece of clothing, only the gun, etc) and then in godot instead of just importing 1 spritesheets, you import the various spritesheets, stack them and then you can change them at runtime to equip different clothes, guns, etc