Thanks Dani, Looking at the relevant cordova API (https://github.com/pwlin/cordova-plugin-file-opener2) it looks like you'd have to know which app opens which file to check if it's installed, and it only works on Android, so I think that's out.
A possibility for an admin interface would be to have an autocomplete field that lets you search for file types by extension/description as defined in tool_filetypes. This keeps it easy to understand, and lets us send a list of "restricted" mimetypes to the app. It also allows sites to add their own specific filetypes to the list if needed by defining custom types in tool_filetypes.
I'll discuss this internally and create a tracker issue.