Type: Null and Silvally are already counted as Legends so they were already going in.
The Ultras will get a side chapter where the MC goes into Ultra Wormholes to find and fuck them, he won't capture them since they technically belong in other worlds and not his... I'll think of some excuse for why he catches Necrozma though
Viewing post in The Legendary Pokemon Breeder comments
I feel like it's fairly easy to justify catching Necrozma.
1. She is likely to be one of a kind, unlike other beasts
2. She is ecologically important as the source of light for Z-Moves and Ultra Space as a whole
3. She is in the black crystal form because she was injured and contained/imprisoned by the ancient form of the Ultra Recon Squad. A while ago it was suggested that that something about how the MC fuckee Solgaleo and Lunala allowed him to alleviate that pain.