Forgot one item,
(5) The Illiridan (sp?) leader started with Trader and Emergent. I did something or other, possibly it was building the Bone Palace, and was offered the Ingenuity trait, which I accepted. It may possibly have been the same turn, or if not, it was really, really soon after, that I either discovered a religion or built my first bit of the Altar, darned if I know what I did, but I got a popup about getting the Spiritual Trait, and getting rid of the Minor trait. I accepted it because I'm a scoundrel, but I am pretty sure I never had the Minor trait... I had Emergent, which is different. I don't know if maybe the progression was:
Trader, Emergent
Trader, Ingenuity, Minor
Trader, Ingenuity, Spiritual
or
Trader, Emergent
Trader, Ingenuity
Trader, Ingenuity, Spiritual (i.e., nothing being "replaced" from above).
Anyhow, I do not have a save which goes back that far, but it sort of felt like I was "double dipping" on extra traits, I really do think it all took place during the same turn which might've fooled the game, don't know. Maybe however Emergent transforms into Minor and the Minor is capable of replacement, really don't know what happened, ought have paid better attention.