I also like the term manufactory, so I'm not in favour of changing the default there.
However, if you find the term unacceptable, navigate to your AI War directory and open Language/en/ships.xml
Change
...
<ln id="CrystalManufactory_Full">Crystal Manufactory</ln>
...
<ln id="MetalManufactory_Full">Metal Manufactory</ln>
...
To
...
<ln id="CrystalManufactory_Full">Crystal Transmuter</ln>
...
<ln id="MetalManufactory_Full">Metal Transmuter</ln>
...
Note that you'll have to do this each time a patch overwrites the language files.