Due to the fact that it can alter time and history and The Red Guy had been playing around with it, the Primordial Soup from the episode, Time Machine, is the reason why there are supposedly multiple Red Guys.
At first there is a case of Fridge Logic. If The Red Guy had been fooling around with the Primordial Soup, why wasn't Cow and Chicken affected nor why hasn't he used it to erase them from existence. That is until I realizes that there are two reasons for this:
1) The Red Guy takes serious pleasure in making the two siblings suffer and leaving them unaffected while everyone they know and love are is one of them. Or he actually enjoys their company.
2) The second possible reason is that even he is afraid of altering history or at least too much of it that could effectively harm him. In an episode from I.M. Weasel (a spin-off from the main show and actual part of the Cow and Chicken universe), I.R. Baboon proves that there are things that can be altered from changing time and others can't since they are part of a Stable Time Loop. Baboon did his part in eliminating the Dinosaurs to ensure humanities' existence but altered the destiny of onion rings which results in The Red Guy suffering intense pain from getting his face splashed with hot onion rings oil. Maybe The Red Guy did attempt to eliminate Cow and Chicken but no matter how much he tried, they are still there.
The Weasel episode also shows an alternate reason how The Red Guy got to the Primordial soup. He stole Weasel's time machine and went back.
Cow's birth cow was a surrogate for Mom and Dad. This is one of those universes where humans and talking animals coexist without question (a la Get Fuzzy); Mom and Dad are animal lovers (as are their family), so they decided to have animal children instead of human children. Chicken, they hatched from an egg, but Cow was arranged through a surrogate cow - this explains Red Guy's flashback of him delivering, "Mom's baby," even though she was out in the waiting with Dad the whole time.
In the episode "Chicken in the Bathroom", Mom, Dad, and Cow are spurting out Unusual Euphemism's for going to the toilet. Most of them make no sense (eg I need to make peace with the Germans). But Mom's euphemism "I need to resolve a family conflict" actually makes sense, because the family was conflicting (her, Dad, and Cow wanted to use the bathroom, he didn't want them to while he was in the tub, and despite being in the tub he didn't want to take a bath, but they wanted him to take a bath), and if Mom used the bathroom she could help solve it as it would be one less person who needed the bathroom and she might in the process think of something to get Chicken to take a bath. Also, Dad's euphemism that he has to "jump the gun" kind of makes sense, too, because Chicken was saying that the bathroom was off-limits until he took the bath and that the family had to wait. If Dad went to the bathroom before that he would, according to Chicken, be using the bathroom too soon and therefore "jumping the gun" as we understand that idiom to mean.
In the episode Cow's Dream Catcher, Cow has a fear of being milked by the Milkman. It makes sense when you remember what happened in her previous jobs. In her first job, she learned her boss nearly sent her brother to his death and at her other job, she was about to be milked to death by the King and Queen of Cheese. That was a terrifying experience, especially that she was a child during all those occurrences.
Red threatened to wash Chicken's mouth with soup. Now soap may sound more cruel, but what if the soup used had chicken stock (or chicken broth) in it?
This is another case of Furry Confusion: in a bumper for Cartoon Network, Chicken confesses to eating beef when looped into Wonder Woman's lasso of truth, not to mention Cow has been seen eating poultry before. On top of that, both Cow and Chicken frequently eat pork products, whether in the form of weenies, sausages, or ham... and they have a cousin who's a sow.