The answer to question 1 is no, at least for now. As the plugin currently works, the Draw Dataset plugin doesn't transform the atlas data to the space of the dataset (with the exception of transforming back to the orig/native space from a standard space). That's in contrast with the way whereami works, transforming coordinates when the transformations are available.
If you want to use an atlas from another space, you can either transform the dataset to match the space of the atlas, or, more likely, transform the atlas to match the space of the dataset. For MNI, TLRC and MNI_ANAT spaces, these transformations are all stored in AFNI in the AFNI_atlas_spaces.niml file and shown with whereami -show_xforms. There are a number of messageboard postings on how to go among TLRC/MNI/MNI_ANAT spaces, but let us know if you run into any problems.
The MNI_ANAT space is a shifted version of the MNI space. The spaces are described in the class materials here:
http://afni.nimh.nih.gov/pub/dist/edu/latest/afni10_volreg_talairach/
