For me it seems more logical the parts diagram than the shop manual. As you say, the angle of the plate seems more "straight" with regard to the plunger.
I read the "Zen and the art of motorcycle maintenance" a few months ago. Can't forget a paragraph about shop manuals. It went on the line of "normally, in the factory, skilled people is busy in the design room or the prototyping. When the time comes for the manuals, they will find anybody who is not busy to do the job". That is, you can't never really trust official manuals at 100% because the ones who write them are not the same than the ones who designed or built the product.
What about the engine mounting bolts? In general, it doesnt make any difference. It all depends in where do you like the nuts to be seen. You can either put all of them in the same place, or alternate so the number of heads and nuts is even. For example, in the CB350 twin, the lower engine bolts have the nuts facing inwards. From a mechanical point of view, it wouldn't make any difference. From an aesthetic point of view, it's a nicer view the bolt head than the nut.