Thanks Martin!
So after updating the shader to use discard instead of setting the transparency to 0, it looks a lot better.
Before:
After:
There is still an issue with some areas because they are already using semi transparent materials (wind screen etc)
This is likely be due to the render order issue mentioned before. A quick-ish fix to this is to have all the transparent parts of the model on a separate mesh instance/mesh in your modelling package before exporting.
That way on load, you can set the render component for that mesh to be renderer last after the rest of the ship.