Eagle pcb and schematic reference designs on github are incorrect.
Reference nRF52840 pcb schematics and layouts are exactly the same for examples 2-6. I believe each is a copy of var4. The schematics for these reference designs are listed correctly in the specification document but do not match what is included here.
shas for the files mentioned:
33e3b6ec2ab9c637af923696b05402c14a7aad5f ./nRF52840_qiaa_var4/nRF52840_qfaa_var4.brd
33e3b6ec2ab9c637af923696b05402c14a7aad5f ./nRF52840_qiaa_var3/nRF52840_qfaa_var3.brd
33e3b6ec2ab9c637af923696b05402c14a7aad5f ./nRF52840_qiaa_var6/nRF52840_qfaa_var6.brd
33e3b6ec2ab9c637af923696b05402c14a7aad5f ./nRF52840_qiaa_var5/nRF52840_qfaa_var5.brd
33e3b6ec2ab9c637af923696b05402c14a7aad5f ./nRF52840_qiaa_var2/nRF52840_qfaa_var2.brd
5277508d2408c335e8cf7c6b7b72fe56d11456ea ./nRF52840_qiaa_var1/nRF52840_qfaa_var1.brd
10e51c58db4f37b49d97fa6383e1ded67b908e7d ./nRF52840_qiaa_var4/nRF52840_qfaa_var4.sch
10e51c58db4f37b49d97fa6383e1ded67b908e7d ./nRF52840_qiaa_var3/nRF52840_qfaa_var3.sch
10e51c58db4f37b49d97fa6383e1ded67b908e7d ./nRF52840_qiaa_var6/nRF52840_qfaa_var6.sch
10e51c58db4f37b49d97fa6383e1ded67b908e7d ./nRF52840_qiaa_var5/nRF52840_qfaa_var5.sch
10e51c58db4f37b49d97fa6383e1ded67b908e7d ./nRF52840_qiaa_var2/nRF52840_qfaa_var2.sch
02e48d1517dd5b4ccd6796172df9c5c0e61a0596 ./nRF52840_qiaa_var1/nRF52840_qfaa_var1.sch
Here's a link to the documentation on infocenter:
https://infocenter.nordicsemi.com/topic/ps_nrf52840/ref_circuitry.html?cp=3_0_0_6_2