That is correct. I have done several intakes on 4.6L and 5.4L engines, all the replacement gaskets are like that, as well as many of the factory ones.
Keep in mind, there are dozens of variations in the modular Ford engines and hundreds if not thousands of changes in applications. Running a shop for years, we have yet to see the exact same configuration twice. They can only make so many gaskets.
That being said, make sure everything lines up, look for defects, verify all the ports are sealed, and torque all the bolts to spec. Do this and you will not have an intake leak, at least not related to any work you did.