There are three areas, for 2K, 3K and 5K point levels.
The general text file has something like:
Racial traits 1 count := 3
Racial traits 1 choice 1:= advanced propulsion
Racial traits 1 choice 2:= natural merchants
Racial traits 1 choice 3:= normal
(Look for this structure, I know that the wording is totally wrong)
Change choice 2 to 3, and 3 to 2, then you're done.
What happens is that the rage use every Last racial point available, and once the first two traits are chosen, SE4 sees that 0 points remain, and quits. It dosen't notice the fact that Normal costs 0.
When you put normal up higher in the list, It gets chosen before the AI runs out of racial points.
At least, that's how I think the guts of AI racial setup work
.