Hi David,
This is not written that both command are supposed to return same results :)
The single command line way is more correct from a Maven point of view since SonarQube plugin will be able to "see" all source folders (including the one added dynamically by other plugins during generate-source phase for example).
In the two command line way, mvn sonar:sonar will only see "default" source folders.
The Maven model do not make distinction for generated code, so you have to manually tell SQ to exclude your generated code. Another option would be to add a default exclusion on target/** or maybe hardcode to exclude **/*generated*/** but I'm a bit afraid of the possible consequences.
++
Julien