Is there a conflict between FAR 4.1005-1(a)(5)(I), which requires unit and total price on all FFP deliverable lines unless an exception applies; and FAR16.505(b)(3), which suggests that IDIQ orders may not be priced in advance on the base IDIQ?
This answer is only based on the information provided in the question. I think you answered your own question when you stated FAR 4.1005-1(a)(5)(i) requires unit and total price unless an exception applies. In those situations where an exception applies you may not see the unit and total price in the base IDIQ contract.
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From the information provided in the background you state the base IDIQ prices or elements of total price cannot be established in advance, but the KO has a compelling business case as to why they cannot be established. In this case the KO might want to look at requesting a deviation from the FAR following FAR 1.4.