forum.freeciv.org

Yes, traits are initialized before the game starts for all players the same way, just it in theory for human ones they do nothing (until the control is handed to an AI).

So. One thing I was thinking of was using certain Trait combinations to help the AI decide which bonus would go for. If I just made them an effect of the traits, could I manufacture a way that a player can control his own, and therefore decide which of the bonuses they want?

Really, it seems to me that there is no way to set up traits from the UI; you can only manipulate them with Lua, but no user-friendly input methods are developed yet. You can use nation set with preset trait combinations (one has been posted somewhere on this forum) and run the game with "Fixed" traits.

Added a feature request for this.