Not sure who gave the order on Nick Rizzuto Jr, but it seems kind of obvious that the ball starts rolling as soon as Montagna sets foot in Montreal. He probably realized that unless he starts taking control of the city and brings the Rizzuto family under the Bonnanos, his days as underboss were probably numbered. Also at this point I'm not even sure if the Cotroni faction acted on their own. The top dog of that group was Joe Di Maulo, and he probably didn't wanna make a move unless he had good enough support to do so. Montagna showed up, and the Violi's in Hamilton were rising stars, so with Vito away, the time felt right. Had they succeeded, I think the family would have restored its ties to the Bonnanos.

Also the other thing you need to realize is that the Violi brothers are Luppinos by blood through their mother, even if they were not made at the time, they were already significant Mob figures given their deep Mafia heritage on both sides of the family. North of the border your bloodline matters a lot more than some random Godfather doing some random ceremony. So when it's said that Montagna met with them in Hamilton, it's safe to assume that he met with the Luppinos in general.