(I looked in trunk for a solution and in the issues for a request but couldn't find anything, I'm sorry if this is a duplicate or already solved)
Knowing the markup used in the js would allow setting the correct markup/function for the added buttons directly in the js.
While there are a few other possibilities to achieve this (load different js files from the plugins depending on the selected markup, this adds complexity on the js side either because of duplication, loading 2 files for the markup-specific and common code, and so on).
The simplest change we could come up with would be to add a line similar to:
to source:/tags/3.1.0/lib/redmine/wiki_formatting/textile/helper.rb#L35, the same for markdown.