In doing some extra reading about markdown I have found this site particularly enlightening.
This is, I think, the original description of markdown, as cited by the commonmark team, and it reveals that a core element of why markdown does what it does is due to its proximity to html.
For instance the first sentence there is:
Markdown is a text-to-HTML conversion tool for web writers.
And I think that some of these quirks of markdown may be less due to their organizational properties and more to a desire to cleanly convert the text to corresponding html code.
This explains why whitespace is trimmed, because html trims its whitespace.
Also the reason for turning any sequence of numbers into an increasing numbered list becomes a little clearer with:
So markdown doesn’t even bother looking at the numbers, because ordered lists in html don’t bother assigning numbers. (The actual code in markdown-it does check the character in the first position, but only to start the numbering from that character).
I think there may be more to it beyond this, (such as formatting consistency across multiple devices) but some of the quirkier aspects do seem very html inspired.