The one significant limitation of the obfuscated UberJar with respect to SCR Generation is that SCR XML files cannot be generated for components which extends an obsfucated abstract class. For example, if you have a workflow process which extends com.day.cq.dam.commons.process.AbstractAssetWorkflowProcess, that will not currently work. You will need the unobsfucated version. We continue to evaluate the impact of this issue and are assessing possible solutions