When running coverage and specifying a source directory, if you would like to omit a submodule using the --omit flag, it is ignored by run.
If you add the omit definition to a configuration file under the [run] section, it appears that it respects it, however, it doesn't actually it's just that both REPORT and HTML read the omit definition of the [run] part of the configuration file.
If you remove the configuration file, then don't actually run coverage again, but rather just generate a report, you can see that the "omitted" folder was still processed.
I have attached an example module along with a bash script for demonstrating the issue (reproduce.sh). In this example, I am attempting to ignore test_module/contrib.