Some of this has to mesh or be resolved with the 5 year jump.
Technically that is the loop hole, but the other thing is:
most likely the FF will emerge 'full-blown' from the confines of some other property. Like the Antman 3 thing, with Kang and timey-wimey stuff.
If this happens, as often has happened in the MCU, the origins will not be that similar or consistent with the comic.
Steve should have ended up with Sharon Carter, is the best example of not following the comic, to me.
So the FF may possibly be lost in time/space when they arrive. My guess would be that their origin will be tied to secret/Shield/Pym stuff that just happened to take place around November 1961, and they vanished back then and were forgotten or were never revealed largely to the public.
They avoid the "family out of time" meme because it is clear they're adventurers of a cosmic nature. Maybe we'll see subtle tie ins or cameos that place them in various movies and we see the Rama Tut thing when they went to Egypt, or maybe or something that will link them to Skrulls and maybe Super Skrull in particular.
So I expect or think that we'll get an overview of their adventures, mostly off earth or off 'now'. They've been around, but we never knew it because they were in far flung time or space.
Maybe that is about Dr. Doom. Or maybe we see them just doing explory things; finding the Negative Zone, or other things.
If they do that, than it looks like they've been around a while and Johnny would probably not be that young, as Peter. Especially if the fan wish for casting Reed and Sue are that married couple John & Emily. That would make Johnny more like a teenage son, than younger brother of Sue.