One is a parts catalog, and should not be used as an assembly guide. And absolutely every service manual I've ever spent a great deal of time with contains errors. (Don't ever lap your valves on that bike, for instance). Then too, people fail to read the entire book, for obvious reasons, I suppose, and mistakes are made a s a result.
In any case, the fact is that regardless of any illustration or other information to the contrary, the O-ring goes IN the counterbored recess. This prevents it from being crushed or split by being compressed between the two cases, keeps it from slipping out of position or expanding, and prevents it from holding the two cases apart, all of which would create a leak.
With regard to bolt length, that's not too hard to sort out on your own. There will always be some uniformity to the amount of thread contact they all have, for one thing, but here's a tip:
Looking at the Yamaha
, the bolt part numbers will tell you how long each bolt is and how many are needed. For example, that cover calls for 1 PN 95022-06040
-00 and 7 95022-06030
-00. The bold section of the number tells you that the 95022-06040-00 is an 6 mm bolt (M6x1.0) that is 40mm long. The others are M6x1.0x30mm.