The result out of 3dAllineate here is actually an oblique image sitting inside a cardinal grid of values. In general, if you have aligned the datasets, then you can safely ignore the warning messages or turn them off with AFNI_NO_OBLIQUITY_WARNING set to YES. If deobliquing doesn't produce reasonable results on the original input files, before any alignment, then it may be that the datasets have incorrect obliquity information that has typically been gleaned from sometimes obscure DICOM files. I would try the "3dWarp -card2oblique" option to oblique one dataset to another dataset's obliquity, again only for original datasets. That is a useful step for assessing original alignment and obliquity information.