I saw that document a while ago - that is just the Naval Postgraduate School, located in Bethesda at Walter Reed. Those specialties it has listed (if you train in endo, perio, prosth, pathology, radiology, 2 year comprehensive, etc. in the Navy it can only be done in Bethesda). Notice it doesn't include any of the 3 OMS programs (San Diego, Norfolk, Bethesda) or any of the GPR or AEGD programs, across the country. I assume the GPR and AEGD programs just fall under the dental department at their respective military hospital/clinic. The oral surgery programs may fall under the dental department, or even GME department, at their respective sites too. Also, see that the Navy doesn't have its own programs for orthodontics or pediatric residency..so if they don't get already trained orthos and pedos, it's possible, but very rare (since the need isn't that high) that they can put you into a civilian program.
Oral/Maxillofacial Surgery falls under the Directorate of Surgical Services (or equivalent) at each of the three hospitals. NPDS is an entirely separate entity.
And it's not rare for them to train ortho and pedo, they train some every year or two, outservice. Several other Navy specialties (most notably exodontia and operative dentistry) are not trained at Bethesda either.
The 4 year OMS is the only OMS the Navy offers currently to my knowledge. There are several people in 6 year civilian OMS programs but the OMS is not training any new 6 years at this current time and all NAVY OMS programs are 4 years at this point.