Hi Nick,
I'd hate to make 3dAllineate attempt alignments that are potentially quite far off, especially when the transform to MNI space should be available somewhere in that pipeline. If you just can't get your hands on it, you can go with the parameters you set if they work well with the data you have. I would expect you might have some problems every now and then and the process as you mentioned already will be unpleasantly slower…
cheers,
z