i know its probably a dumb question but here it goes

why are some box different than others? do they effect the vehicles performance?

here what im talking about:
http://www.installuniversity.com/
or
http://www.ls1fun.com/

on the first box it has a section toward the back (closer to MAF) but other doesnt have that section.

 

Can you put links to the exact pictures you're referring to. I can't find anything out airbox lids on ls1fun.com's website.

 

I think you are comparing stock to aftermarket air lids. The stock ones have the baffles that are right in front of the MAF.