Randomly, I used to date a squirty girl who would occasionally go onto b vitamins whenever "a health craze" washed over her. For those that don't know, b vitamins make your pee very orange-y (because your body processes them and removes them via excretion). Well, whenever she was on B vitamins, her ejaculate would be orangish as well.
Sometimes when I squirt, if I am dehydrated or am trying particularly hard (the two often go hand in hand) it smells faintly of urine.
It *does* come out of the urethra (although from glands right near the end of the urethra) so it's not so hard to imagine "contamination" (for lack of a better word), I figure.
And I do think this is part of the reason the "but its just pee" explanation continues to exist.