I have tried to generate effective pom on sample application using mvn help:effective-pom command. http://books.sonatype.com/mvnref-book/reference/pom-relationships-sect-po
If I remember correctly, effective POM means the actual POM to be used.
Incorporating settings in super POM is part of it. It also includes a lot other things, like applying parent POM, applying profiles, substituting properties, and etc.
I think it will be better if you can give some snippet of the settings you thought that comes from no where, so that we can identify where do they come from.