Measuring chain length on a 1x12 I'm installing a Shimano 1x12 setup and following the instructions. When measuring the chain it says to put the chain around the largest sprocket and largest chainring, measure to the zero point, and add 5 links + the quick link (for a hardtail). 

Does this mean the chain is not meant to be run through the pulleys when measuring the chain length? 

Here are the instructions I'm following - https://si.shimano.com/pdfs/dm/DM-MARD001-02-ENG.pdf
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.