Bast*** "Machine Shops/Engine Rebuilders" !

I believe the 318 Poly had dowels for the timing chain cover- the '65 FSM would have been referring to that since LA 318s didn't happen until '68.
As far as the bolt with the oil hole, I wouldn't lose too much sleep over it. Even Ma Mopar couldn't decide if it was worthwhile. I've had virgin small blocks apart that used 4 standard bolts, 3 bolts with an oil drip rail and a bent "finger" to go into the fourth hole, or four bolts with one drilled. When using the factory timing chain tensioner (V6) on a small block (which replaces the cam plate), it's only drilled for 3 holes to begin with... My impression? Chrysler saw no difference over the years and eventually phased it out. So, as long as it's apart, put it back together whichever way makes you comfortable and forget about it.