reStructuredText is very committed to the plain text visually matching the formatted. For headings, visual underlining makes sense in that context. And code is conventionally indented, so it also makes a lot of sense. (Blockquotes are indented as well, differing from code blocks by the absence of `::` at the end of the preceding paragraph; indentation again matches conventional appearance. But that’s a place where I get where Markdown’s coming from, using > indentation like in emails.)
In more recent times, convenience of writing has become a more important concern to people, because these formats have shifted from niche use by dedicated people in real text editors that would like what they see to match the end result fairly well, to mainstream use in textareas and similar, and sometimes even WYSIWYG editors. That’s what’s driven people to prefer the convenience of code fencing, because indenting each line in a textarea is a pain. Ditto on headings. If reStructuredText were being redone now, I think it’s fair to say that prefix rather than underlined headers would be at least an option. It would just remain to be seen whether they went with `###` meaning level 3 even if there was no `##` or `#`, or whether they’d boost it up to level 1 or title, as appropriate.