I think the main problem is that the “mule” plugin, which is not provided by SonarSource, does not support what you want to achieve. This plugin is kind of incompatible with SonarSource XML analyzer: that’s explicitly stated by their documentation where they mention that “SonarQube already comes with an XML plugin”.
The SonarQube API already makes it possible for a plugin to raise issues on any source file without requiring users to associate all possible file suffixes to this plugin. I suppose that the authors of the mule plugin are not aware of that. As a user of this plugin, you should explain your problem to them. SonarSource cannot fix the mule plugin.