There is virtually no difference between run-time solution and build time solution in wro4j. The CssDataUriPreProcessor is responsible for converting image url's into css data uri. In order to use it with maven plugin, just add this processor to the list of processors to be applied. Example:
preProcessors=cssImport,cssDataUri,jsMin,cssMin
Notice the "cssDataUri" alais in the list of configured pre processors. Once added, it should be applied for each pre processed resource.