its not plot holes
im pretty sure it's going to be explained later
and what pile of plotholes are you talking about
I doubt its going to get explained. Obito released the Juubi's final form, yet he still remained the Juubi's Jinchuuriki, on top of the fact that the Juubi was brought back at less than full power (since Naruto and Bee still had they're Bijuu).
The Tree began to bloom, despite the fact that Obito still had all of the Bijuu inside of him. If the Tree could bloom without the Bijuu, then the whole reason for this war and collecting all the Bijuu in the first place completely falls apart.
Even when the Bijuu were ripped out of Obito, the damn Tree STILL continued to bloom (If you paid close attention, Naruto stood ontop of a fully realized flower/tree at the end of chapter 655. Last time I checked that Tree wasn't opened like that prior to Obito's defeat (I could be wrong on that one though)
And there are many "plot holes" in this series, though it may be more fair to call them controversies.
