I've found the differences to be pretty small overall. But the pipeline I currently work with is to take the two anatomical (MPRAGE/MEMPRAGE) scans and put them both into Freesurfer. Depending on your theoretical interests, you could do this in the longitudinal pipeline or as two inputs to the same recon-all (in the more traditional model of dealing with motion). I then run @SUMA_Make_Spec_FS on either that longitudinal template or "two input" output and grab the brain.nii for use with my afni_proc.py commands (using the -anat_has_skull no).

For DWI/DTI, I also collect a T2 image, that I then SkullStrip and align to the brain.nii file. I then run TORTOISE on my DWI file with the T2 as my "structural" file. Some info about this is written out here. If you don't have a T2, you can use the T1, though you have to turn off some of the DWI distortion correction things in TORTOISE. I'd say that's decent motivation to start collecting a T2, and also blip-up/blip-down DWI data.

Using this method, I have my structural MRI (sMRI), fMRI, and DWI/DTI all in similar space.