this is a long standing deficiency of the Mentor tools. Right now you have to make two separate stackups. One for simulation/calculations/documentation and the other for PCB. Having a different stackup in PCB also shows incorrect values for diff pairs, as you have to use the one with the correct stackup.
Having said that I would ask you to support idea D12505 Improve Expedition to allow to have more prepregs between copper layers
as Mentor keeps this idea still "under consideration", where by supporting this idea we could move them to implement it.
Thanks for the answer.
I already supported this idea on August 28 2013.
Sad to see that this item is (2 years ) still "under consideration".