compensation for calculation of safe harbor match

We administer a safe harbor 401K  with Roth only deferrals.

W-2, boxes 1 & 5 are the same dollar amount,  employee deferred $5,000.

Wouldn't the deferral (whether Roth or not) be added to box 5 for the calculation of the safe harbor match??

I'm going from memory here - the Roth deferrals are already included in Box 1, so there are no deferrals to "add back" in to Box 1 if it is just Roth. So I would expect the Box 5 amounts to be the same, in the absence of any other modifications. If you add the Roth deferrals back in, you'd be overstating Box 5. At least that's my recollection, but don't trust my memory - you'll want to look at the instructions.

I hope, by your comment, you mean that simply by chance the only deferrals in the plan happen to be Roth

according to the IRS Q and A https://www.irs.gov/retirement-plans/retirement-plans-faqs-on-designated-roth-accounts#13

Can a plan offer only designated Roth contributions?

No, in order to provide for designated Roth contributions, a plan must also offer traditional, pre-tax elective contributions.

1 hour ago, Belgarath said:

the Roth deferrals are already included in Box 1, so there are no deferrals to "add back" in to Box 1 if it is just Roth. So I would expect the Box 5 amounts to be the same, in the absence of any other modifications.

This is correct.

Get the payroll report.  Don't use W2s.