I believe it is on there want to do list but for now to do what you want you need to make a MOD

If you are playing as a custom faction and you design and save ships while you are playing that faction, your ships will reappear whenever you play that faction.

The only problem with this is that the custom factions must adopt a ship style that is based on one of the default majors. Therefore, any ship you design for your custom faction will also appear in the shipyards of the faction your ships are based on.

After all that I guess the answer is no. You can't make custom ships for your faction without modding.

So...I'm using the Altarians as my base ships. I create new ships for my custom race. They are saved and available every time I use the custom race. I run into the Altarians, and they may be using my ships? It could be worse. That's really no different than right now. I run into the Altarians and we are using the same ships, lol. Thanks.