Apache Santuario (used by xades4j) does not use the "Id" attribute as the XML Id out of the box. You have to set it explicitly. This behavior was introduced on Santuario's version 1.5. Check this xades4j tests file. The DOMHelper class has helper methods to define XML Ids.
As a side note: that signature is not an enveloped signature, since it is not "inside" the signed element. It is a detached signature. The enveloped signature transform is not needed.