I think you're probably right about the old man DiMeo storyline not being brought in so as not to confuse people. The only time he was ever even mentioned was early in Season 1 and I think it was just once or twice, in passing.

But if what you say about bosses being bosses until they die, are clipped or abdicate, then Junior would still be boss even AFTER he shot Tony in Season 6, pt 1.

Again, unless DiMeo did die and the viewers weren't told about it, Junior was acting boss (eventually in name only) and Tony was street boss (though really in charge) up until the very last episode.