The super six porting of intake manifolds on the naturually aspirated 3.5 makes a difference from all reports, but it is not going to be night and day. I expect the same for the ecoboost 3.5.
Definitely worth tuning for, if the difference creates peaks and valleys in the rev band that were not there before. Just like downpipes can be run without tuning for them, but then you are not getting full benefit.