They exist in the Marvel multiverse, and this story says every universe has a Molecule Man, so yes. That's what the word every means.
Nope, you're wrong. They all go back exactly as long as their histories say, which in most cases is billions of years to the Big Bang. Just because a place is introduced in a story in a particular year doesn't mean that place is not supposed to have existed before that in that fictional setting. From our perspective as readers, yes, of course, but from the perspective of characters in the story, unless they make a habit of breaking the fourth wall like Deadpool or She-Hulk perhaps, the perspective of readers and writers doesn't matter, and those billions of years of history of the newly discovered universe are just as 'real' as their own.