I have to respectfully disagree with you on both of those areas.

First of all, in regards to the plot to kill Gambino and Luchese, we have this taped conversation between Sam DeCavalcante and Joseph LaSelva about Bonanno:

SD: He put Magliocco up to do a lot of things... Like kill Carl.
JS: Well, Magliocco was his son's father-in-law.
SD: He put him up to kill Carl and Tommy Brown.
JS: Well that must have something to do with Profaci's outfit?
SD: Yeah. Now they feel that he poisoned Magliocco. Magliocco didn't die a natural death. Because the only one who could accuse him was Magliocco. See Magliocco confessed to it. But this Joe didn't know how far he went. Understand? So they suspect he used a pill on him - that he's noted for it. So he knows the truth of all the damage he done. But they feel he don't know how much the other people know. He'd come in and deny everything but he knows he couldn't deny he made people when the books were closed.

While I don't believe that Bonanno had Magliocco killed, DeCavalcante certainly talks about Bonanno's involvement with confidence. Magaddino was also caught on tape around this time talking about how Magliocco had confessed to the plot and that Bonanno was possibly involved in it, though one can argue that Magaddino was biased against Bonanno. DeCavalcante, on the other hand, was an advocate for Bonanno and tried hard to settle the situation peacefully. He and Joe Zicarelli were later criticised for advocating on Bonanno's behalf when it became clear that the whole thing would have been easier if he was just killed when the trouble started. DeCavalcante in fact wanted to continue mediating the Bonanno situation until Jerry Catena told him to leave it and divorce himself from the situation. DeCavalcante also had a direct link to Gambino - it was Gambino who personally told him of the Commission's edict to ostracise the entire Bonanno family until Bonanno was removed as boss, John Morales was removed as underboss and Bill Bonanno was removed as consigliere.
I don't trust the denials found in the Bonannos' autobiographies because they were so clearly revisionist and self-serving. That also links to my next point about the 'misunderstanding'.

Bonanno claims he did not go in because he no longer recognised the Commission as an official body because it had not been ratified by vote again at the last general meeting. But what is also obvious is that he is the only member who felt this way and it coincided with Bonanno's more individualistic attempts to branch out into Montreal, Arizona and California (and also in reading his book one gets the clear impression that Bonanno felt he was above everyone else at that time). His legal problems (such as when he was detained in Montreal) did contribute to his not appearing before the Commission but he still had plenty of opportunities to do so. I agree that Bruno and Zerilli messed matters up a bit as all they were instructed to do was to go with DeCavalcante to issue a summons and not tell Bonanno why he was wanted. That led to him only communicating through DeCavalcante, but even that ended poorly when he angrily accused DeCavalcante over the phone of being dishonourable, which led to discussion that Bonanno was becoming unhinged. Bonanno eventually said the Commission should come to him if they wanted to see him and the Commission refused to do so, considering the offences he was accused of and the fact that he had refused multiple summonses through various messengers. It wasn't a misunderstanding as much as it was Bonanno being evasive and obtuse for months.