There is nothing in the story line that accounts for the supernatural abilities of the starting flagship and other ships with survey modules. The flagship requires fairly advance technologies.
I would suggest totally eliminatig the flagship. Start each race with a scout instead. Also requires that anomolies be visible before they can be surveyed.
Unlike GC1, the technology needed for constructing a ship with a survey module is early in the technology tree, so that surveying of anomolies will still occur early in the game.