Sascha Retter thankfuly provided a pull request, which addresses the parent pom in another folder besides other modules. However, if you use multi module builds you usualy have a more nested structure, e.g.
This is not possible right now or with Sascha's pull request, since it only allows for one subdirectory with the same name as the artifact.id. However with his work I was able to produce a crude hack which supports multi module projects.
The hack works by iterating over all reported issues. For each issue the list of gerrit changes is iterated. If a key of the gerrit change contains from the current issues component artifactId/pathToFile the current issues key is modified from pathToFile to the key of the current gerrit change. With component of current issue is groupId:artifactId:pathToFile. Code see attachment. SonarToGerritPublisher.patch
Again, this is only a crude hack and can be improved uppon.
Note: This hack does not work for merge commits since there the entries for the gerrit changes are the commit message and only files edited with the merge commit itself. This does not include files changed on the branches.