Code W means it's either pre-tax money that the employee contributed (deducted from paycheck), the amount the employer contributed that the employee was not taxed on (usually in exchange for the employee signing up for a much cheaper insurance policy with a high deductible), or both.  Since it's already pre-tax, taking a deduction for it on Schedule 1 Line 13 would be double-dipping.  So for all intents and purposes they are treated the same on Form 8889.

If the employee makes an additional contribution outside of payroll, this would be deductible.  I often recommend clients do this if I see that they have not maxed out the benefit.  It's similar to an IRA where you can contribute up to 4/15 for the prior year and take a prior year deduction.

Rick