Mandatory envelope thermal properties

The insulation values in Table 5.5-X are prescriptive, not mandatory. They are already in fact prescriptive and available for trade-off. Only the items in Section 5.4 are mandatory.

Yep Section 5.4.1 can be a bit confusing but if you go to the referenced sections they are all about the requirements for the insulation itself not the quantity.

That's right Katherine,  As a matter of a fact, the credit requires the following: 

1. Comply with the mandatory provisions (Sections 5.4, 6.4, 7.4, 8.4, 9.4 and 10.4) in Standard 90.1-2007.
2. Inclusion of all the energy costs within and associated with the building project.
3. Compare against a baseline building that complies with Appendix G of Standard 90.1-2007.

As you can see, the projects need to comply ONLY with mandatory provisions of ASRHAE 90.1, and be more efficient than an energy model that follows the Appendix G. Consequently, you have plenty of flexibility to design your envelope and MEP systems. Some of the U-values might be more efficient than the baseline (other U-vaues may not be more efficient).... The same applies with MEP systems, for example some spaces might have a LPD be more efficient than the baseline (other spaces may not be more efficient)...etc. I hope that helps!