1.The shinju is not the final form of the juubi,the juubi is a form the shinju took after kaguya and the shinju became one.
There is a major difference.
2.The Juubi is not the Gedo+bijuu.The gedo is the husk(Merely a shell of what was left of Kaguya/Shinju's form as the juubi.)
]This is important to note and ill explain in a moment.]
3.When obito became the host for the "juubi" he reverted the chakras back into its original form the shinju (Kaguya at this point was separated when she was sealed which is why the gedo exist in the first place).(Its for all intents and purposes an incarnation)
Now before i continue there is more than one way to activate IT
A.Eat the fruit and become a pseudo host as kaguya did and awaken the third eye and approach the moon.
B.Become the complete host gain the third eye and directly approach the moon.
C.Use the shinu itself if one does not possess the eye
Regardless of where the power is stored all you need is a connection.
Now concerning obito,Naruto pulled out the tailed beast.He did not pull out the mazou.
The mazou has its essence but was not the main source of power or else obito would of used it from the start instead of collecting the beast.
The reason why madara lost it is because kaguya took over his body and gained all his power.
She was then sealed which means everything she had on her was thus sealed.
Now as for the why shinju did not vanish is because the tree itself at that point was like the Gedo Mazou just a catalyst obito had all the power of the shinju inside him he merely brought out its psychical form to activate IT because he did not have the third eye,though once again obito retained the actual power in him so when he was stripped of its power it too became a husk.
