If the scope of an indirect dependency is changed in the dependencyManagement of your pom, this scope is not correctly taken into account when resolving compileAndRuntimeDependencies. I've created a very minimal testcase to demonstrate this problem:
https://github.com/papegaaij/resolve-dep

This testcase resolves the dependencies using:

File[] jars = Maven.configureResolver().workOffline()
	.loadPomFromFile("pom.xml")
	.importCompileAndRuntimeDependencies().resolve()
	.withTransitivity().as(File.class);

The pom only defines 1 compile dependency (shrinkwrap-impl-base), which depends on 2 others (shrinkwrap-api and shrinkwrap-spi). shrinkwrap-api has a dependencyManagement with scope provided, so I expect this resolution to yield 2 files (base and spi), but it yields all 3.