What is the appendage on the factory air intake pipe??

Those chambers off to the side are resonators to make the intake quieter. Some might be able to hold water too - if they have a drain.

the "front" pressure will be affected as if a different 'racing' air filter was being used. May have to "tweak" the settings electronically? dial it into 1800 ft. if that's possible. It is made from rugged polypropylene (soda bottle mat'l) and molded in black always....come to think of it they should make them in clear!

"Will the insertion of a c/a package defeat whatever purpose this appendage serves?" --- Yes, a free flowing intake will make more noise and provide laminar flow. That's what aftermarket intakes are supposed to do.

As above- It is a noise cancelling device. adding an aftermarket CAI will add air and increase sound. I love my AFE CAI noise is really not an issue.