Note that the operative word in Pub 15-B is exclude, not deduct.
That is a provision to allow employers (not employees) to exclude the excess reimbursement from the W-2, if their plan meets the rules . But if they report it on your W-2, it's taxable income to you. There is no way for you to deduct (or exclude) it on the tax forms. You should not change your W-2. The IRS computers will catch any change and send you a dunning letter.
I believe the reason the word "option" is used, in the rules, is that employer has the duty to determine if the reimbursement meets the rules before excluding it.
You need to ask your employer for a corrected W-2, showing less money in box 1 but the same withholding in box 2. That will get the excess withholding refunded to you when you file.
