I've seen nothing in the files that specify how they do that. However, the titans you see are not real titans. They use a special entity type called "Cosmetic", so what I think the game does is automatically place any  cosmetic entity in the frontend map at the start of the game.

Therefore, if you remove the references to them from the entity.manifest file and the galaxyscenariodef file that should work.

You could also try to get capitalships to display as well as titans.  Good luck, but seeing the titans at the start is nifty.

Following

Did the dev.exe give any errors? Its possible it could be referenced somewhere else.

That said, if worst comes to worst, you could just change the cosmetic entity files to use a single super small polygon mesh, remove the weapons and abilities etc. That way they'd be there, but invisible to the player.