Not everything is reported as added to box 1. In fact. many of the things in box 12 are reporting subtractions from the amount in box 1, not additions. Since these are state laws, the IRS cannot possibly keep up with them all.
So, the result is that the transportation benefit is added to Wages (box 1) on your W-2, so it is taxable on the federal return, and in CA, it is deductible on the state return.
"Are all such lines eligible?" Absolutely not. It depends on what they're for and what state you are in.
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