Generate two coverage reports in a single jenkins build
There's a nice plugin called HTML Publisher Plugin. You can generate HTML coverage reports and publish as much reports as you want under different titles in one Jenkins project.For example I generate html reports using karma+istanbul and then publish them to Jenkins.
On JUnit xml report files. You should import JUnit once enumerating all files probably from different directories but you can differentiate them with proper package names inside files.
If I'm right, you can't use, as a post build action, the same plug-in twice( note that I'm not really sure). I faced this problem when I worked as Jenkins plug-in developer for a company and the solution was to use a plug-in that make the same thing.
For example: for JUnit reports there is an official JUnit plugin and also XUnit. For my problem it was simple.
So, maybe you can find a plug-in that do the same thing as Cobertura or you can change the output format of the java coverage or karma coverage. For example, for java you can use EclEmma or Jacoco...