Hi Michael,
Thanks for sharing your thoughts.
With such a long discussion thread plus a number of tracker issues, it's not easy to find out what has actually been done with regard to indentation in recent versions of Moodle. Thus, I'm just mentioning that in Moodle 4.2 onwards (also 4.1.3 and 4.0.8), you can now indent items one place to the right (or to the left for right-to-left languages) for courses in Topics or Weekly formats.
It's enabled by default in new sites, however for sites upgrading from earlier 4.0 or 4.1 versions it needs to be enabled by a site admin, as described in the doc Upgrading to 4.2.
After the site admin enables it, they have the option to reset indentation previously set (though only one level).
It's possible you could get one level of indentation back!