There is indeed a conflict with [line 404](https://github.com/stefanv/pelican/blob/86595555d54c00c8078eb63a875fa9760cce318a/pelican/readers.py#L404) which will overwrite the`.extensions`. I remember having hesitated to remove this block for `'%s_EXTENSIONS' % fmt` (https://github.com/getpelican/pelican/pull/1011#discussion-diff-5619189), 
In pelican 3.2.1, the setting MD_EXTENSIONS was actually modified by `MarkdownReader.__init__` then the MarkdownReader instance .extensions was overwritten with the setting, so it was working :o