The dowel pins on each end of the block are to hold the 2 end gaskets in place.
He is not using the end gaskets,so they need to be removed. Otherwise the intake will not fit flat on the motor.
The reason you leave the pins in is to align the intake. The reason the holes are not in the intake is it needs to have them drilled after you align the intake. There is a simple procedure to do this. But if you don't believe what I am telling you check this
Set the intake on the motor and see how far you can slide it front and rear without the pins with all the bolts in loose. Now turn the intake upside down and measure the thickness of the web between the two runners. Almost the same as the movement isn't it?? The web in the head and the web in the intake need to be aligned. and these pins insure it stays there during bolt torque. Did you ever think that this could be the reason why some run good and some don't. And maybe some just get lucky.
Just trying to help ya. But I know you have it covered. Steve