arg... thats right... are you changing this for single player mode or Dynavers3? Same settings changes, just in a different directory....
for single player:
Sfc3/MetaAssets/ServerProfiles/Character.gf change your starting ships at the bottom of this document.
If you are setting up a server kit you will need to go into your server kit:
ServerKit/Assets/Scripts/Campaigns/Champaign1.mct to make the mentioned change/check.
It took me trial and error error error, retrial and error error error... before I finaly got it originally... there are enough files interlinked settings wise, that makes it... Interesting at best, to get it done.