1. MNIa is the original version from the Eickhoff-Zilles SPM anatomy toolbox. You don't really need it. If you would like a different list to appear in whereami output, you can set the atlases and the order with the AFNI environment variable AFNI_ATLAS_LIST. This can be optionally set to "ALL" to show all available atlases. Keep in mind that will use more memory.

2. The MNI version is a shifted version, computed by changing the origin and without interpolation. The whereami interface does this transformation behind the scenes when computing the coordinates. By default, the list of coordinates shown in the whereami report is TLRC,MNI,MNI_ANAT. You can control this list also with another AFNI environment variable, AFNI_TEMPLATE_SPACE_LIST.