Hello yo4561, 
My apologies for the delayed response to this post. 
yo4561 Wrote:I have a question on the idiom "Not as X, but as Y".
Let's say I have the following made-up example:
Veronica must consider gardening not as a hobby, but as a job that will help her pay the bills. 
The correct idiom would be 
Not X but Y.  Examples: 
Not running but jogging
Not cats but dogs
Not (as a hobby) but (as a job)
yo4561 Wrote:Question 1: I've seen "comma" placed before the "but as", however why is the comma needed? Why would you use it in this structure? Again, I realize that you should pick bigger issues on the GMAT, but this was a bit strange to me.
You don't necessarily need a comma in the example you provided. Commas are required before conjunctives like "but" when two independent clauses are being connected. 
Examples: 
I like to go to the store, but I only go on Fridays when they offer extra discounts. 
I not only like to draw but also like to paint. 
yo4561 Wrote:Question 2: To clarify on modifiers within parallelism, can you have a modifier(s) for one element but not the other(s)? I see that "that" modifies job, but there is no modifier after "hobby." 
The X and Y in 
Not X But Y are called elements. Having a modifier after one element but not the other is okay, as long as the meaning of the sentence is still clear and the elements themselves are parallel.