For example, why does TeXmacs put the focus box around a bullet character in a list when it does? It seems strange, but invoking the “why” feature would explain the rationale behind it.
Idea: A "why" feature to explain why TeXmacs does something in a particular way
This idea is not bad, but implementing it in the way you suggest would require some work. I think it is easier to start with a FAQ-kind webpage, or help page, which explains some of these “unique” features of TeXmacs, and some basic design decisions which inform all the UI. This could help the new users to pay attention to the right details and use TeXmacs in better and more efficient ways. Suggestions for topics to put in this list?
There are some unintuitive things in bulleted lists and it is still not clear to me whether they need to be that way. In addition to the strange focus issue mentioned above, there is also the issue of allowing multiple bullets on the same line, which happens a lot during editing.
Also, editing in TeXmacs feels very static. Stuff doesn’t restructure much or easily. For example, there is no automatic merging of identical adjacent environments. Why not? Also, why can’t one easily change the indentation of an item in bulleted lists?
I think you are underestimating the fun that you would have in getting the TeXmacs editor to do that 