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The chakra of the Bijuu is simply being transmitted to Obito's Pain Rikudou through the Gedo Mazo's chakra chains. Sealing the paths won't seal the Bijuu itself.
We saw him use the full bijuu in battle though. That makes me think that the chakra wasn't remote, but that they were pulled our of gedou temporarily. Didn't he have Gedou swallow them back up as well? My memory's a bit fuzzy.