CEL and tunes ?

I keep seeing ppl here having issues with the CEL and upgrades.

Downpipe
JB4 tunes
Racechip
Intakes


I understand if the factory ecu is seeing different variables for performance installed parts, so i have a couple questions:

1. If aftermarket hardware part is installed (downpipe, intake,exhaust), why does the ecu throw a code, and can it be cleared properly ?

2. Any tune added (JB4, Racechip, etx) installed, this is possibly more understandable to throw a code, and can it be cleared ?

3. And, upon CEL appearing..... If the code is not cleared & left alone, does it affect performance ???? ie.... Limp mode ?

4. And does clearing code with JB4 etc, only clear it from the dash light, or clear it in ecu. And once cleared, can it / or will it return periodically ?

Thanks,
:)