Don't be confused by that; the Navy is buying the aircraft, the Marines do not buy their own equipment as a separate service - it is all blue dollars.
USMC does have their own Systems Command at Quantico and do buy their own "equipment", but it is largely relegated to ground systems. The so-called blue dollars in support of "green" (USMC) are not only related to aviation procurement. They cover medical and religious programs as well as Seabees. There are even Green dollars in support of blue. The Marines do not turn everything over to Navy in that regard. NAVAIR is totally integrated with Marine representation in programs that they care about and in cases of platfroms that are Marine specific like H-1 Upgrades (AH-1Z+UH-1Y, V-22, AV-8B, etc.), the program manager is almost always a Marine Colonel. In fact, JSF recently got the second Marine general assigned to the front office as a deputy who will fleet up to running the show (PEO JSF alternates between Air Force, Navy, Marine management). That general came from role as AV-8B Program Manager.
However, USMC "POMs" for their people, but as stated above most (almost all)* of Marine Aviation is paid by Blue dollars "programmed" by OPNAV N88. DC Air is dual-hatted as N88M and there are Marines integrated into the OPNAV N88 staff for every platform they operate as well as DC Air APW/APB staff watching out for USMC interests and building the Marine Aviation Campaign Plan. Under the TACAIR Integration Plan, USMC squadrons are integrated into Navy Air Wings to meet commitments and some Navy squadrons fulfill USMC commitments.
*Air Defense and C2 are paid for by Green Dollars