Solutions
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Mr.Quiggles's post in GTAIV CVPI ELS Rear White Strobe Issue, fix? was marked as the answerWas able to create both the actual rear light texture transparent, and the light flashing to it transparent. So it just has the color of the trunk behind it because it is the trunk. I had to make the actual texture of the light transparent because then there would be a black flashing light on top of it which was distracting.
So it all worked out. :)