X, Y ,and Z --> all 3 should be parallel
Agreed.
X, Y and Z --> Y and Z should be parallel
If Y and Z are parallel, then what's the function of X? I guess Y and Z could be parallel modifiers of X. It's a bit confusing to make abstract constructions such as these without any examples.
X ,and Y --> X and Y are independent clauses, hence no parallelism issue here
I disagree. Sometimes with 2 items, we can use a comma before the and. This takes place if there's an intervening modifier, or if the sentence is long and would be clearer with a comma. For example: 'At the zoo I saw parrots with beautiful plumage flying around the aviary, and chimpanzees.' Another example: 'At the restaurant we ordered steak, and fish and chips.' Since 'fish and chips' is basically one item, it's probably clearer if we add a comma before 'and'.
X and Y --> X and Y should be parallel
Agreed.
Remember that commas have lots of different functions, and that constructing a sentence is about finding a way to convey meaning clearly. Also, GMAT definitely does not test comma usage, as the rules around it are so controversial.