I'd like to suggest that org.jboss.shrinkwrap.resolver.impl.maven.archive.plugins.CompilerPluginConfiguration should support the "encoding" property of the maven-compiler-plugin just like it supports "source" and "target".
I know that you can use "compilerArgs" to pass any parameter but that wouldn't be obvious when you have this special "encoding" parameter in maven-compiler-plugin. Everyone would expect that this setting is passed on.
And things can really go wrong in all magic ways if you compile your files with the wrong encoding...