I'd say that's a matter of lawyerism and interpretion of rules that don't state it explicitly enough. As far as I know you can only have one trait of a given type. That "type" could be interpreted as campaign/faith/religion etc. traits or..traits giving the same thing.
There's also the thing with bonuses of the same kind not stacking unless specifically noted - that in turn could be interpreted as trait bonuses not stacking..so you might have two traits giving the same bonus, but only benefitting from one at a time.
You can't have two campaign traits because you can only take one trait per category.
Apart from that it depends on the kind of bonus the trait gives. Most give trait bonuses and those do not stack. So having two traits that give a trait bonus to initiative would not work.
