I'm not with the state department so I can't obviously say for sure but maybe if say it occurred on base, it's not considered "In Japan" as far as the the state is concerned? Sort of like how APO addresses are still technically considered US addresses.
I think I can explain this.
Under 22 U.S. Code § 2715b "[w]henever a United States citizen or national dies abroad, a consular officer shall endeavor to notify, or assist the Secretary of State in notifying, the next of kin or legal guardian as soon as possible, except that, in the case of death of any Peace Corps volunteer (within the meaning of
section 2504(a) of this title), any member of the Armed Forces, any dependent of such a volunteer or member, or any Department of Defense employee, the consular officer shall assist the Peace Corps or the appropriate military authorities, as the case may be, in making such notifications."
www.law.cornell.edu
The state department's reporting requirement under 22 U.S. Code § 2729 would be closely tied to their duties to issue reports of death. So for service members who die from non-natural causes overseas, the information regarding those deaths as well as the reports of death, would probably be handled by the military instead of the State Department.
Also, this is why I doubt that the data is incomplete for June. The State Department is continuously issuing reports of death and these reports would be compiled to create the public reports. So it's likely that the two months of time taken by the State is used to ensure that they actually have all of the information from May and June. I know we're talking about a government bureaucracy, but it doesn't take two months to compile, anonymize and approve a report on data that they should already have in a database, especially when they know that they need to issue it every 6 months.