I've seen the ones you're talking about and decided to measure them: the caps are bored (molded, actually) larger than the bottom parts of the bearings. This makes perfect sense and is a good way to make a universal cap, because I have yet to see an upper cap with journal-worn marks on one. They run fine, since the cam never 'jumps upward' unless the cam chain gets so loose that it could actually jump time (I HAVE seen that..., from a broken tensioner roller during a roadrace), at which point the cam could jump around a bit.
I think Honda simply decided to make them less expensively by molding the lower bearing journals slightly "high" and then milled them down to an accurate diameter, which is completely possible today, given modern CNC equipment. In the 1970s, not so much.