Board Thread:Naruto Discussions/@comment-24048522-20191229052502/@comment-1210805-20200102095737

The key word in the databook entry is integrated.

[Kaguya] integrated with the God Tree and challenged the twins to battle...

Integration means combination, amalgamation, unification, merger, fusing, blending and so on. Regardless of what her children thought, the databook makes clear that what actually happened is that she merged with the tree.