>>34342273>>34342363>>34342382Nebby's permission is implied since it has no reason to forsake its own well-being just to listen to Lillie. The only thing that suggests the fusion has any ill effects on Nebby is the Pokedex, which has never been a definitive source of information. For all we know Nebby might sympathize with Necrozma or even simply just enjoy being part of it, especially when it transforms into the Winged Dragon of Ra.
That being said they really should have included at the very least a line about Nebby wanting to do it or it not harming Nebby or something like that. Ideally the fusion should have just been an innate ability of Necrozma rather than being achieved by machines. For Kyurem it was fine since the implication was that they wanted to become whole anyway, but it's a lot less certain with Nebby and Necrozma.