Obito knows about ashura and indra and how they transmigrated to Naruto and Sasuke, he could of easily took Sasuke's chakra when he implanted his EMS and he could of easily took chakra from Naruto when he gave him the Kyuubi.
Obito wanted Naruto and Sasuke to fight each other because "faith had them next in line". He knew full well that Ashura and Indra are inside Naruto/Sasuke.
Lol, all speculation and zero facts.
OT: Read the manga OP.
1. Ashura and Indra left Madara and Hashirama the moment they died. Ashura's chakra won't be in Hashirama's genetic material as it had already moved on from him, so getting his DNA after his death won't do anything.
2. Even if they did still contain it, Black Zetsu doesn't contain Madara's chakra. Chakra and Will are two completely different things.
3. The Sage outright GAVE him the Rinnegan. That is a manga fact, so don't try and dispute it. Naruto got the Senjutsu of the Six Paths and the Mark on his hand while Sasuke got a mark and the Rinnegan in his left eye.
Obito is not going to obtain the Rinnegan. I don't know what to say if you Obito fans really believe this.