the eye to eye does not affect the travel. the fact that the dhx3.0 that comes on the expert model has a cartridge which allows the shock to compress more than the vanilla r on the bighit does. thats why you get an extra 0.9" of travel on the expert.
my expert came stock with a fox vanilla dhx3.0

 the difference in travel is only because of the different rear shocks installed on the bikes.
the expert comes with a vanilla rc while the fsr only has a vanilla r without the cartridge