@Steven I wanted to give an update. I think my issue is just the bounding box. I just need to resize(i.e. add zero-padding) to match the MNI dimensions. (This thread seems to be about the same issue).
I’m not sure how to do this without warping or resampling my image. I tried different settings with MCFLIRT but I had no luck. I guess something like mrgrid that you recommended here may be what’s needed, but I don’t wanna install a whole toolkit to this. This also sounds like a neat trick that would accomplish something similar, but i don’t know whether the image will end up being centered the same way as the MNI template.