In Xoom Console and Settings Migration Tool you can choose whether or not to include dependencies when retrieving configuration. Your decision will depend on the use-case.
When transporting configuration it is recommended you include dependencies, as, if they do not exist in the target system, you will end up with a configuration containing bad references.
Conversely, if your aim is to compare subsets of configuration, as with configuration versioning, including dependencies adds unnecessary information and tends to obscure the comparison you are trying to make.
In a scenario where different development teams are using sharply defined queries to work on non-overlapping subsets of configuration, including dependencies in a retrieval and subsequent deployment could cause some settings on the target system to be overwritten. See topic on separating concerns.