You are correct that in a properly designed spin echo pulse sequence, where sampling occurs at the moment 2*(TE/2), fat and water will be in phase. This is because the fat/water chemical shift IS a T2’ effect that may be compensated by the spin echo. To achieve out of phase images, the timing of TE would have to be altered. GRE is most widely used for Dixon imaging, but spin echo-based methods have also been created.