There would only be a conflict if the ALPA President tried to intrude on individual MEC negotiations and tell them how they are going to negotiate their agreements. As you know, that doesn't happen. He just signs what is put in front of him, unless it violates an ALPA policy in the Administrative Manual or Constitutional & Bylaws.
The reality is that each MEC negotiates their own CBAs without any interference or direction from ALPA International. As long as that is true, any claims of a conflict of interest are patently false.