If you're seeing that FICA was withheld, I would be confident the 'self-employment' aka FICA was paid through employer contribution as well as the withholding.  Do the amounts for SS/Med you see withheld match 7.65% of the wages AND housing allowance (which should not be in box 1).

I have one clergy client who arranged this with his church, so I suppose if the employer is willing....

And in this case, no need to make adjustments on the S/E worksheet.