As far as I understand it, the wiki-like format is actually quite different from the wiki format (as in your wiki module).
The issue arose because I realised that when my students were using the moodle auto-format to build a glossary, which I use a lot (I teach French for Science and Technology...), exporting the glossary was a nightmare as the
XML file did not include paragraph tags.
The markdown format looks very appealing, and can be used in most moodle activities. I don't think that my students will have any problem learning it. And no more need to type in html tags, which really slows down the writing.
So I am thinking of pushing them to use the markdown format almost everywhere. But then, when it comes to the wikis, this means having to learn a new format again. Mind you, it may not be a huge problem, but it could be a bit confusing, if not overwhelming for first year students (although the students come to me to learn French, they come out of my course fluent in html, wiki and markdown...).
Perhaps the solution would be to replace the wiki-like format by the proper wiki format in all activities...
In any case, this will be an on-going issue in our place... It will be interesting to see which format the whole university adopts for communicating via moodle.
Françoise