reflections are always the biggest problem in car audio--no matter what freq.
with the immediate sound wave reflecting off the back window, there is always a chance that it could result in a easier-locatable sub(if you're going for sq, it's a bad idea)..
the other thing to keep in mind is the distortion of the sub. if you put a sub in front of you, and crank it up until it audibly distorts, or sounds bad, and then do the same thing, but turn the sub so it is reflecting off a wall, so you are hearing the reflectiong sound wave, it will sound cleaner, because the reflection will cove up some of the nasty stuff.
while the 2 paragraphs seem to contradict each other a little, they are both true..
because the glass is so smooth, pointing the sub at a 45deg angle to it, means that EVERY sound that the sub makes gets reflected directly towards you.. when you point the sub mostly at a carpeted surface, some of those nasty effects get absorbed, so when the sound gets to you those nasty artifacts are removed-- too a extent..
this is why so many setups have the subs pointed at the back of the trunk instead of the front..
anyways, i don't believe the baffle should be a huge deal-- as long as you use large, rounded edges, the baffle it-self, should not affect sound quality..