I mean, did fans ever perceive the stories as taking place in separate continuities? I understand that they did exist separately for a good while. Eventually that changed. But did very many people think of that way?
Originally, seeing young Clark delivering good with a horse and wagon was kinda surreal to me. I mean, Superman starts in an era when there are more cars than horses (and in a city, which makes a difference). And it was in the midst of an era of heavy change (which in retrospect we sort of think of culminating in or immediately after WWII in the United States) and 20 years could make a heck of difference. In reading the old Superboy comics, though (and I've only read a limited number), I don't always get sense of time. Sometimes the stories seem set further back, and sometimes the characters seem to be wearing contemporary fashions. Similar issues with appliances.
I have to admit, the idea that they would have ever thought fans would generally treat Superboy as not a (retconned) part of the past of the Superman they were also reading seems strange. I may try to find old letter pages, but those are so late in Superboy's existence. Odd, really, since I don't think of anyone would have ever had any thinking-them-the-same issues with Earth 2 Superman, even if they kinda were originally the same (even if I'm not fond of dividing out Earth Two and One versions of characters by taking part of Golden Age and saying it's a different person when I thought of those as either early installment weirdness or still part of the characters' histories).
I don't suppose there are any fan-pages out there that track the era-specific-indications in different issues of Superboy stories, are there? Could be kinda fun.