Ah, after reading the new DD I've got it. Fully operational ruler customization is kinda locked for only one origin.
A bit weird decision, isn't it?
Imagine if the starting species trait limit is set to 1 point and can be expanded only by Overtuned origin. The ability to pick negative traits is also exclusive Overtuned feature. That is exactly how the ruler customization feels now.
I think the focus is supposed to be on training up your initially inexperienced leaders during the game (including whoever serves as ruler), more than picking one who already has the right skills. If you want your ruler to be the Main Character from day one, you pick the origin.
Where I would hope for more customization though is with Gestalt "rulers" (who obviously can't take the Under One Rule origin). The "ruler" in that case isn't a leader in the normal sense, they're supposed to represent the aggregate "personality" of your entire empire, and given that Gestalts generally have fewer characteristics on empire creation (no ethics, fewer civic options), it would be a good place to give them more character.
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