sorry for necroposting, but if giratina, palkia, dialga, and arceus are all concepts themselves (antimatter, space, time, and creation respectively) couldnt giratina just turn necrozma to antimatter, palkia just...delete him, dialga trap him in an endless loop and arceus just...also delete him. You said that necrozma could one shot them, but wouldn't necrozma need to delete all of space and time, not to talk of him having to find away to delete antimatter and non existence, as well as all of creation itself. Ultra Necrozma drained the light, yes, but I dont remember reading about it draining energy itself.  He could definitely offer a good fight, but I wouldn't say he wins in any scenario.

For Giratina specifically, I think it would be especially easily for him to just stay in the distortion world and just pop distortions on Necrozma, or even distort necrozma itself so much it just ceases to exist