I've encountered something like this before where the Draw Dataset display seems to have a small bug if you change the view between tlrc and orig after you have started the plugin. If you switch the view before starting the plugin, the atlas ROIs should be displayed correctly. Aside from that, auto talairaching doesn't produce a perfect correspondence of structures, so there will be some difference.

You might considering displaying the atlas ROIs in different ways in AFNI. One way is to right click on the image and select "Show Atlas Colors". The menu there, along with the Show TT regions checkbox in the Overlay panel, will allow you to display the ROIs from the TT Daemon.

For other atlases and templates, you can display these as datasets which are usually stored in the AFNI binary directory. Set the environment variable AFNI_GLOBAL_SESSION to be that directory, and the atlas and template datasets will be selectable in the Underlay and Overlay choosers.

Most AFNI programs can use atlas datasets as input. Here is a simple example to apply an atlas mask to another dataset.

3dcalc -a dset+tlrc. -b 'TT_Daemon::amygdala' -expr 'a * step(b)' -prefix 'roi_mask_amyg'

The whereami program can be used to generate mask datasets from atlas ROIs.

whereami -mask_atlas_region 'TT_Daemon::Hipp' -prefix testhipp

Check the documentation here for some more information:
[afni.nimh.nih.gov]
[afni.nimh.nih.gov]