Status of Independent EMBs

An interesting question arose in my mind at a recent training in Brussels. International agencies that sign technical assistance agreements with EMBs, strive to gain an invitation from these EMBs. These agreements are separate (though may be the same) as may be signed with the host government. Does this agreement with the EMB elevate the institution to another sphere of governance, similar to the Executive, Legislature or Judiciary? Although these agreements may serve simply to have a formal endorsement from the inviting EMB, it does raise the question of the exact status of independent EMBs. Are we creating separate governance structures through these actions. What do you think?