Yes, fiberglass would be a smoother install and cleaner bass response due to the lack of corners. However I hate to fiberglass and I'm not good at it.
Putting the box in the side panel would not be efficient. Cleaner look but as for bass response there is not enough air flow for a 10" sub. So then the box will have to be build outward from the panel which still will take up space.
As far as taking up space in the truck, I think it's a perfect fit. Its all wasted space plus the amp spot fits inside the extra space the box hangs over.
I am not worried about fitting a 12" sub. I have plenty of mid snap coming from my amazing Focal 165KR 2 ways. I really do not have a need for a sub but a 10" done properly will clean up the sound allowing just the correct amount of bass to highs. If I were to put a 12" sub I would need to upgrade the doors to either a STRONGER 6" (but what affordable speaker am I going to get rated above 150 rms that sound goods) or just upgrade to 8" high. Relocating the door speakers would also help.
In this 4runner I am looking for great balanced sound at normal listening volume. I have an Avalon which has all that music crap inside to go deaf. 2-15" subs thru a crossover. 2-10" highs, 2-8" highs, 2-6" highs, 4-tweeters powered individually from its own amp. 4-amp, 3-batt. AND Fully Matted. I still think I want to get rid of the 6's and add 2 more 8's or 10's due to crazy amount of deafness I go thru in that car i cant hear the words no more.
^^^reason y I'm keeping the 4Runner simple.