I dont know the full story between what happened with Nintendo and Sony, but i do know that Nintendo werent the only ones saying no to Sony, Sega said no to them as well. Clearly there is more to it than Nintendo just packing up and leaving, there is speculation Sony wanted more and both Nintendo and Sega forseen Sonys plans. Who knows and this is not the topic.
However if what you say is true than sure Nintendo broke that code but we dont know the full backstory, we only know from the outside. Now this is about Square moving one of the most established IPs and locking it exclusivity to a rival conpetitors platform. Thats why Nintendo was pissed.
I dont understand how Sunset Overdrive is even comparable to this type of move. If Ratchet and Clank crossed to Xbox than id see your point, but your point on a new IP that Sony didnt want is not the same as Final Fantasy.
I recall Sony wanted more control than Nintendo was comfortable with. I don't think Phillips felt wronged. They made a deal with Nintendo for Hotel Mario. 3 Zelda games and Super Mario World 2: Wacky Worlds. The last one was canned mid-development. Lol seeing how bad those games were. I'd say Phillips was the one in the wrong.
As for SEGA. Don't put much faith in that being on Sony. SEGA of Japan constantly made awful decisions and was very stubborn. SEGA of America often had better ideas to do things but SOJ always overruled them and made things worse.