So my own take on this is that it's not really about atonal music at all. The musical universe in which this is presented (certainly in the article I referenced) is already using 12TET, and where a specific scale (of the 4096 possible) has a known name in 1 or more cultures, it is cited (this includes the western "church mode" names that you mentioned).
It's still unclear how much "tonal music" is simply a shared set of cultural assumptions and practices, and how much arises from acoustic physics and acoustic perception. So ... rather than a priori priviledging a specific group of interval sets ("major", "minor" plus "a few modes"), why not start by exploring the full universe of all possible (12TET) interval sets (aka "scales"). By using an explicitly mathematical approach one can bring some analysis techniques to bear on the "full universe" that are not readily available when stuck in traditional western theory and notation. To me, this approach accomplishes two things. The first is that it offers a bridge to non-western musical traditions. The second is that it offers a common core from which to understand both "tonal" and "atonal" music, particularly their similarities and differences.
Finally, its a particular bug of mine when people connect "modes" and "scales" as you do in the your final sentence. What is important in (almost) all musical traditions are not the specific notes used to form the pitches that make a piece of music, but the intervals between the pitches, and their ordering. There's significant evidence that we are vastly more sensitive to relative pitch (intervals) than absolute pitch - play the same series of intervals starting from a different tonic/root and we experience it in almost the same way. Change the interval series (i.e. the scale), and we hear a much more noticeable difference. So, the major scale is just an interval series, and the "modes of the major scale" are also just interval series. There is no inherent relationship between them, other than one can construct them by rotation. The modes do not "belong" to the major or minor scales, nor vice versa (indeed, in fact the major and minor scale are just modes too ... just an interval series).
And now really finally: we actually don't have special names for most of the possible interval series that can constructed from the diatonic notes. We have a very limited number, and from my reading and understanding it is unclear if the ones we have names for are priviledged by physics and perception, or are mostly the result of historical precedent.
It's still unclear how much "tonal music" is simply a shared set of cultural assumptions and practices, and how much arises from acoustic physics and acoustic perception. So ... rather than a priori priviledging a specific group of interval sets ("major", "minor" plus "a few modes"), why not start by exploring the full universe of all possible (12TET) interval sets (aka "scales"). By using an explicitly mathematical approach one can bring some analysis techniques to bear on the "full universe" that are not readily available when stuck in traditional western theory and notation. To me, this approach accomplishes two things. The first is that it offers a bridge to non-western musical traditions. The second is that it offers a common core from which to understand both "tonal" and "atonal" music, particularly their similarities and differences.
Finally, its a particular bug of mine when people connect "modes" and "scales" as you do in the your final sentence. What is important in (almost) all musical traditions are not the specific notes used to form the pitches that make a piece of music, but the intervals between the pitches, and their ordering. There's significant evidence that we are vastly more sensitive to relative pitch (intervals) than absolute pitch - play the same series of intervals starting from a different tonic/root and we experience it in almost the same way. Change the interval series (i.e. the scale), and we hear a much more noticeable difference. So, the major scale is just an interval series, and the "modes of the major scale" are also just interval series. There is no inherent relationship between them, other than one can construct them by rotation. The modes do not "belong" to the major or minor scales, nor vice versa (indeed, in fact the major and minor scale are just modes too ... just an interval series).
And now really finally: we actually don't have special names for most of the possible interval series that can constructed from the diatonic notes. We have a very limited number, and from my reading and understanding it is unclear if the ones we have names for are priviledged by physics and perception, or are mostly the result of historical precedent.