Because the Air Force version can't land on the mini-carriers used by the Marines. (Neither can the Navy version, for that matter).
Better question is why the Navy couldn't use the Marine version, and build cheaper, smaller, carriers. The USS Ford cost over $16 billion, they've been working on it over 6 years, and it is supposed to be ready in a couple of months, and is an easy target for the Russians or Chinese - even, perhaps, the Australians.
Because the Marine version cannot carry the load, fuel capacity, speed nor range for the Navy. Jarheads need about 200 A-10’s and throw in a couple hundred OV-10 Broncho’s.
For $16 Billion you get 75 combat aircraft
https://en.wikipedia.org/wiki/USS_Gerald_R._Ford
For $1.432 Billion (1989 price ($750 million) inflation adjusted for 2016, it is probably more like $2 to $2.5 billion) you get an LHD with between 6 to 20 AV-8Bs depending on the specific amphibious assault ship class (LHA/LHD)and the mission configuration. MEUs typically have 6-8 AV-8Bs; when specifically designated to conduct “Harrier Carrier” operations (Sea Control), the ships can have up to 20 AV-8Bs.
Keep in mind that the USS Ford is the class leader for a new class of large aircraft carriers and a substantial part of the $16 billion is all the upfront engineering and research and development cost that won’t be expended for later ships of the class.
Among other things that you don’t get with the “smaller” LHA/LHD option is the aviation fuel bunker and the bomb/missile magazine capacity of the latest “full size” aircraft carriers. You also don’t get the very sizable aviation ordnance, fuel, and maintenance divisions needed to keep up with around the clock, continuous flight operations. All this requires space for things and space for people that only the big bird farms can supply. An interesting operational planning/integration issue will occur when the shorter-ranged Marine squadrons are periodically deployed aboard CVBGs as part of routine air group squadron rotations. As is often pointed out, Marines may fly the aircraft but the Navy pays for them.
One last point, during full scale war against a capable naval adversary (something we haven’t had to do for awhile), the Amphibious Squadrons and Groups that LHAs and LHDs are part of will require continuous air, surface, and subsurface protection. They must have outside escort. By contrast, a carrier battle group (CVBG) is a complete offensive package that can defend itself and others when called upon.