By a separate box of the W-2, I assume that you are referring to box 14?
FTB Publication 1001 says "Enter the amount of ridesharing fringe benefits received and included in federal income on Schedule CA (540), Part I, Section A or Schedule CA (540NR), Part II, Section A, line 1, column B."
So, the first statement may be true ("Are employer transportation benefits deductible in CA if they're only included in wages"), but I can't address the second statement, ("but not listed in a separate box of W-2?") because I don't know which box you are referring to nor do I know if these benefits are included in Wages.
If you are not referring to box 14, please come back and tell us.
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