I think the same argument can be made for almost every "the machine knows better than the user" decision, so it seems to me that this is pointing out that the Markdown list behaviour should be tarred with exactly the same brush.

This is true of all these features in general. They're all well-intentioned. No one wants to design a system that annoys users. But my criteria is meant to illustrate why it might not have been a smart idea to begin with: the user didn't indicate they wanted the system to renumber their bullet points. In fact, very often the user indicates that they want a specific numbering by placing specific numbers. The feature would work if there was some way to indicate this is just a bulleted list with numbers. Instead, the system assumes 100% of the time that the user made an error, then fixes that error in a way that is difficult to detect without ever providing feedback about the changes. That's a bad system that happens to usually be trivial or at most embarrassing. But the design itself is flawed from first principles.

A better way to implement auto-numbered lists would be indicate you want to use auto-numbered lists, just like you indicate you want to use headings, links, or any other element. First, don't rewrite all numbers, making the fact that a correction is taking place under the hood invisible to even experienced users. Auto-numbered lists should be indicated by having multiple lines starting with, say, "<space>0.", or even better "<space>#." to be more congruent with the use of "#" for headings and subheadings in other markdown systems (languages?). Second, when a user submits a post, the system should indicate what has been changed, perhaps with a non-intrusive highlight.

The problem would never have arisen had the developers asked my two questions "did the user indicate X?" and "where/how did the user indicate X?"

I suppose you should add onto that "is the change transparent to the user?" which is also known to cause some potentially life-threatening errors: http://www.dkriesel.com/en/blog/2013/0802_xerox-workcentres_... - you probably think "it's markdown, what's the big deal?", but who knows. Maybe someone gets some medical or chemistry advice and, sure, they shouldn't trust reddit, but then maybe someone dies anyway. So I think it's always best practice to indicate that a change has been made.