Honestly it could go either way with what Minato was thinking. All I know is that his thoughts went from this (ch.502 page 10):
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to this (page 11):
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so one of the points that lead him to the conclusion that the masked man would be Madara, was that he was capable of using s/t techs. We can't really disregard it.
ps. I'd like to add to this the fact that Tobi was trained by Madara. He learned how to use space time tech from Madara. Even if it was Obito's original ability from his sharingan, Madara was the one that made it possible for him to advance in s/t technique so that he is on the level that makes Minato say this:
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Obito can't get onto a level higher than Tobirama without being taught by a teacher stronger than Tobirama: Madara. So there's a strong hint that says that Madara knew s/t.