The 1966 and 1998 versions of the Emcee are not exactly comparable. He's much more of a presence threaded through the entire production in the revision and staging of the '98 version, whereas he pops up periodically for the ironic "limbo" numbers in the original '66 version. So I'd say it was right that the role was considered supporting at the 1967 Tonys and leading at the 1998 Tonys.
As for Che, it probably should have been considered a leading role in 1980, but perhaps the producers of Evita didn't want Patinkin competing with the heavily favored Jim Dale in Barnum or Mickey Rooney in Sugar Babies. Good as Patinkin was in Evita, I don't think he would have won against Dale, who carried Barnum on his shoulders and was great in it.
Begin at the beginning and go on till you come to the end: then stop.