Can the judge merge the agreement even if my spouse and I agree that it should be incorporated?

Yes, it is possible that the judge will not go along with your agreement on this issue. A court’s final order or decision can supersede the terms of the agreement.

If your agreement is clear, fair, and appears to be freely negotiated, furthermore your desire for incorporation rather than merger is clear, fair, explicit and is not illegal or does not violate any contract laws it is likely that the judge will accept your wishes.