If Jiraiya can get information about Akatsuki (and to that of Madara's "summoning") then the 4th can probably have done the same.
Thinking that Madara was a threat and would have made a move (say, he -Minato- was one of the few people who had an idea that Madara can summon the Kyuubi) against Konoha, the fourth had planned ahead of what to do. In which case, he developed the Shiki Fuujin in preparation for such.
Think : Naruto is about to be born in say, 5 months... or 4 perhaps. Then around this time, Minato had the information about Madara. He then thinks of a way to counter the Kyuubi. He develops the Shiki Fuujin (thinking that he would seal the Kyuubi with him and die with it), but then when Madara's threat became more imminent (at the same time that Naruto will be born in a few months / weeks / days... the fourth thought of another plan. "If I can do something about the separation of Yin and Yang chakras, then I might as well seal the Yang to my son if he gets born in time, if not, I'll die with all of the Kyuubi anyway. If this separation plan succeeds, it may save Konoha in the future."
If I was a bit too much or disorganized, I'll repost when I get some sleep (haven't slept in 20 hours... and counting).
Arbitrary, seriously, you're overthinking this and making a lot of assumptions. I hope you went and got some sleep.