Wolverine was heavily referenced in 2005's Fantastic Four. Do you think it was possible that those movies were set in the original timeline and when Wolverine went back in time, he caused the newly created revised timeline to have a new iteration of the F4 as seen in FAN4STIC?
My bet is the first two movies WERE set in the original timeline and the reboot is set in the revised timeline.
Even long before the third MCU film released, Fox was planning on doing a Civil War movie with its Marvel characters as far back as when Origins went into production. They were gonna pit Daredevil, X-Men (including Deadpool), F4 and all related licensed characters against each other. So considering this AND the scrapped F4 reboot sequence in DP2, I'd pretty much say the movies ARE set within the Fox multiverse.
What do yall say?