depending on where you use fiberglass and how you finish it, the effects aren't always terrible.
A LOT of competitor vehicles have fiberglass panels, or some even have full fiberglass interiors.
When you're designing a system for competition, its more of a engineering task then just making things look pretty.
You take into account reflections and how in designing the pieces of the car will best utilize that phenomena.
In the trunk its not a big deal since the bass sound wave is reflected off the back wall of the trunk anyway. The reflection of that wave which moves back towards the front of the car is what creates the highly desired Bass Up Front illusion. Whereas the sound of the bass source is perceived to be coming from infront of the passengers despite the actual subwoofer being in the back of the car.
As for the interior of the car, you already have a lot of reflective surfaces that can colorate and distort a desired sound stage. However, this is where experimentation comes in with speaker angles.
Don't be afraid to use fiberglass. Just focus on what your project goals are and don't heistate to experiment and take your time in finding the best possible setup that produces the sound you want.
... its just like dialing in your car for performance.. better tuning takes time.
good luck.