1-No, SECA would have no amounts in boxes 3 through 6 so you would be required to pay both halves of the self employment tax. You are on a FICA standard because they are taking social security and medicare payments out of your check. You already know that you owe SE tax on your housing allowance.
2-It depends on the type of retirement plan that you have. You should look at the type of retirement plan that the church is giving you. A traditional 401k would raise the amount in boxes 3 and 5 by the amount on 12D as you figured so the retirement plan is not a traditional 401k.
However, the outside firm is correct. You should enter the W2 exactly as it has been issued to you because that is what the IRS has. They will kick back your return if it doesn't match. I would continue to question the payroll, however, because it doesn't sound like they're doing it correctly.
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