Just re-watched a little bit of Game 7 from the 1960 World Series on youtube-- I can only stand a little at a time given that the wrong team won.
Anyway, I noted that the announcer called him Roberto when he came to the plate.
I grew up in an American League area during that time, and only saw the NL occasionally on TV. Like every other kid playing in the sandlots, backyards and parks, though, we all tried to emulate our favorite players and debated who was best. Not once in those instances did any of us refer to "Bob" Clemente. Small and maybe irrelevant sample, I know, but just sayin. Don't know where we were getting our information, but it was always Roberto. Oh, and we all collected baseball cards too.
Like the inimitable Mr. Spaeth observed, it is strange Topps got it right for the first two years and then changed the name. I could see it if the player requested or maybe if it just became common knowledge that's how he was called (e.g. John then "Boog" Powell), but that's not what happened here, and there is some evidence the player did not like the name Topps assigned to him. One wonders why the company changed it back to Roberto so many years later as well.
The OP made the observation that seemingly every other card manufacturer during the time got it right (although Transogram had one of each). Fair question as to why Topps went the other way, and IMO the other posters' takes on possible reasons seem legitimate.