That website sums up what I thought was generally accepted as having happened
"As Arum put it, “Professional wrestlers are performers. The thing is a fraud.”
However, Inoki had not planned to put on a show. To him and his manager, it was a serious fight between a boxer and a wrestler. "
Basically it was supposed to be 3 pro wrestling matches, then Ali's camp either found out or suspected Inoki (who is a complete ****ing tool, just for the record) would make it a shoot (which he did). Ali's camp came for a pro wrestling bout and didn't want to get into an NHB match with a multi million dollar investment in a country they didn't care about, so they came up with the rules that made it so awful.
I don't know if this is 100% true, but thats pretty much the sum of what I've heard on the subject.