My general feeling is:  If audiences believe people can shrink to the size of an ant or turn green and incredibly strong, or burst into flames etc. is it really too much of a stretch to believe some superheroes existed before and nobody bothered mentioning them?
I can see trying to keep things relatively neat, but when it comes to telling a story the way they want to tell it, I'm going to let them do it and not get hung up if I have to suspend disbelief on some of the timelines.
It will be interesting to see what they do with Captain Marvel.  Will she be much more secretive and the Skrulls never be known by the general public?  If so, okay, they're keeping with the idea that superheroes and aliens weren't well-known prior to Iron-Man.
But if she's out and proud, that pretty much smashes any barriers to the FF.  In fact, they will probably have time to throw some mentions of FF into the final cut of Captain Marvel if they want to go the retro route.