I think you are right, the dont even show on the schematics as they think that those bolts are not to be touched.Just looked at mine, which are original.
They are indeed safety torx bolts.
Why Yamaha shows them as hex head (above links I posted), IDK. Cap bolts, using the above part #' is fine.
Their only security bolts to keep someone from dinking with them as there's NO REASON to touch them. (They hold the two frame halves together..)
My 07 frame, pic just taken: