It's an optional money sink that allows a little bit more freedom in making your ship unique. And from what I've seen (which is admittedly only the inventory of one base so far) The engine names and descriptions look more like
"BX-12 Fighter Engine"
rather than
"Werewolf Engine"
It could really go either way though. You could keep all the engine names and descriptions generic so they don't identify as belonging to a specific faction. Or the other way would be fine too, and we'd have pewpew over 'Y U USE ENGN WITOUT PERMISHUN! DAI THEF!"