underlayless was the wrong word, but yes - it was using itself as an underlay with very bad intensity ranges. I desire my blobs to be on brains, not empty black space! Unfortunate that this processing strips away all the friendly AFNI information, but it is at least correctable.

It looks like afni_proc used 3drefit on the data, but only changed the view and not the space, according to the limited history that came with the combine+tlrc file. I'll run 3drefit based on my volreg data (tlrc view, but MNI space) that was used as input to tedana - tedana does not perform any spatial shifts, thankfully.

Appreciate the clarification - happy to have figured out the source of all these problems finally.