Measuring chain length on a 1x12
Don't run the chain through the derailleur. The Shimano instructions would explicitly tell you to do that and the diagrams would also show it.

In general the chain does not have to be run through the derailleur when measuring length. See this Park Tool video. This is because the chain takes a fairly straight path through the derailleur cage when on the largest chainring/sprocket. It's recommended to do it this way to avoid getting whipped in the face with the chain. 

The Shimano instructions say to add more links than the Park Tool video, but I'm sure that's to take account of Shimano's specific 1x12 drivetrain design.