I'm used to working for a full time employer and having a separate line on my pay stub for expense reimbursement that I do not pay taxes on.

I am trying to evaluate a W2 contract which would have an all-inclusive rate where I would pay for any travel expenses. I believe if I work 1099 these can be deducted, but is this also true in a W2 contract situation, or would I end up paying income tax on the additional pay amount that is supposed to cover travel as if it were regular income?