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.