Grouping istanbul code coverage report by folder
Can't you redirect the output to the same folder, i.e. unify the folder holding all results?
This might help!
Or maybe instead of Instabul alone, try adding NYC too as:
My .babelrc file looks like this
{ "presets": ["es2015", "stage-2"], "plugins": [ [ "istanbul","NYC", {"exclude": ["**/tests/*.js"]} ] ]}