I sort of agree. For the time being, geany could default to treat .edn as clojure file. People who may dislike doing so, could perhaps have an option to disassocate .edn then (but I assume not many may want this).
I do not know the internals of geany well enough, but a simple advanced option could suffice for people to edit all associated filetypes, via a simple widget. This widget could be populated with these default file type associations, and people who would dislike that, could edit it.
I assume that most people using .edn are people having an interest in clojure too. I never even saw a file ending with .edn so far in my life. :) The usual extensions I use are ...
.xml .rb .py .txt .md .gen .cgi .pdf .odt
Where .gen is a "custom" format I use to generate other files, usually .md files. I think the above list covers about ... 95% of text files or text-like files I may tend to use/modify at the least sometimes.