It would be interesting to look at the fossil record for Krypton. One of my favorite elements of L. Sprague de Camp's "Viagens" books is that his Krishnans have a Neanderthal or Homo erectus sub-race that survived: as scattered forest-dwelling tailed people. I can TOTALLY see something like that being a "World of Krypton" backup.
Also, it's not 100% sure that Kryptonians evolved on their planet; even discounting Bates's story, in LEGION there's some amusing debate whether Krypton or Daxam is the colony.
There's the Zelkot and Volkir stuff in DC Comics Presents #1/#2.
Would you be more inclined to believe in a God if your race clearly came in from somewhere else and hadn't clearly evolved with the other species on the planet?
That doesn't seem to stop people on this Earth.
Anyway, it is really hard to explain why they look so much like humans and for that matter all those others races in the Legion do as well, storyline wise anyway.
In real life, the reason was of course is it was done for marketing reasons. Little boys and girls could relate more to aliens that looked like them rather that some odd looking creature. This is why only alien villains look like monsters. Of course they are some rather disturbing racial subtexts to this "those who look different than us are evil" mentality. This was the same reason why Japanese people in WW2 era comics look like vampires and grotesque sub-humans.
Martian Manhunter was the 1st one to change all of this.
Star Wars made it cool to have Aliens who look like Aliens who were good guys.