Pretty funny actually - compare carefully the input and output 
Looks like some of the prefix whitespace is expanded on lines #2 and later.
What does babelmark say: http://johnmacfarlane.net/babelmark2/
Here’s the test I’m using
----A----x----B----x----x----HEAD
\
x----x----C
And here are the test results.
Just realize the test I pasted above doesn’t render right when viewed in the topic, the source is actually:
Markdown seems pretty unanimous about how to treat that 
and we are doing the right thing.
If you want a monospace font in your editor go for that, by adding a site customization.
I am torn, my personal pref is for monospace markdown textareas, but there is a strong argument monospace makes this “more computery” and “less friendly”. Ultimately this is a decision that is up to @codinghorror. Even cooking Stack Exchange uses monospace (but on the other hand they do not display stuff side by side).
----A----x----B----x----x----HEAD
\
x----x----C
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We are not interested in changing the font of the editor to monospace