As far as the Luchese family after Tommy died, I always assumed that the close relationship that he had with Carlo Gambino gave the Gambinos a leg up on influencing that family after he died. As you mentioned Eboli complains in the Mary Farrell docs about Luchese and Gambino conspiring against him with Genovese away in jail and Catena across the Hudson and not particularly interested in sticking his nose into NY day to day affairs. Also, the marriage between Gambino's son and Luchese's daughter seemed to seal the deal.
Philly is interesting because from what I have read it seemed that Vito Genovese was very close with Bruno's predecessor, Joseph Ida, which was evidenced by the fact that they were stopped in the same car leaving Barbara's property after the Appalachian meeting. I have also read that Catena and Bruno were very close, so I have always thought that the Gambino's influence over Philly really started after Catena retired to Florida in the early 70's, but I could be wrong.
As for Costello's consigliere, I have not looked into that too much, but I always thought of him as being like Giancanna, a guy who did not really care about having a formal structure in place, as long as everyone was making money. The guy Pandolo sounds suspicious because he does not seem to show up anywhere else other than in reference to being Costello's consigliere.
Adonis is really interesting, like Costello and Genovese he was an original and had power that transcended any position that he might hold in the family. One reason that I would think that Moretti got the underboss spot over him and Genovese is that just as Genovese seemed to pick Catena because he was the most powerful guy in the NJ wing when he was boss, Moretti was the most powerful guy in NJ when Costello was boss. Also, I think that I read somewhere that Moretti was Costello's cousin. As for Adonis, I know that he was eventually deported, so maybe his legal problems prevented him from assuming that role, or maybe he didn't want the job and instead wanted to have a role like Jimmy Alo had, more of a floating power that was left alone to run his own rackets wherever they may be and make gobs of money.
As for Miranda, he was very powerful in a couple of boroughs, as I think his crew was actually at least in part based in Brooklyn. No matter what position he held he was highly respected, as he sat as an equal at the table with big bosses like Gambino, Trafficante and Marcello. The attendees at that meeting were really interesting, I would have loved to have been a fly on the wall before the meeting was broken up.