it could well be that the functionality in this (point 1) is currently broken – we’ll investigate and hopefully push fixes to github soon.
Re 2. – not really but you can easily create your own atlases (i.e. combine two) by just creating a new folder with the according nifti files inside (don’t mind the ea_atlas_index.mat and the gm_mask nifti file, these will be generated upon first visualization of the atlas).
3. 2D view is neurological convention (meaning left is left and right is right). Instead, some other programs follow radiological convention (where right is left and left is right, “view from below”). 3D view is not flipped (in 3D it’s all more clear and obvious).