RepositorySystem#resolve(ArtifactResolutionRequest) doesn't use the local repository passed in via the resolution request as target for metadata downloads (pom.xml). It uses the local repository from the settings.xml instead.
After the resolution process there are only the jar file (and their checksums) contained in the "custom" local repository that was set via the resolution request. The pom and parent pom files (and their checksums) could be found in the "global" local repository (configured via settings.xml).
After the resolution process the whole stuff is contained in the "custom" local repository, the "global" one wasn't touched.