That is true, but was that true even before we put the custom bootloaders?
Because IF one had a Qualcomm bootloader and then flashed and got a NOKIA DLOAD, then most probably it was done using NCS. Unless the only way to 'lock' you Qualcomm bootloader is by actually flashing a NOKIA DLOAD ROM using QPST for the first time, and then NCS would work thereafter
We do not even have custom boot loaders at the moment because we do not have a valid private key to create the required associated certificate, but I may be wrong. The Qualcomm loader also requires a certificate, but for the Lumia 710 Nokia has (presumably by error) put the Qualcomm Loader + associated certificate on their firmware repository. Someone got the hands on that before Nokia removed it. So if you got a 710 you can flash the Qualcomm Loader on your phone.
It may be the fact that we overwrite the OS partition with dd that changes something so that NCS refuses to flash. Because indeed it can update from Qualcomm to Nokia DLOAD BL. Or maybe the supplied Qualcomm Loader is an very early version that never got on a production phone and therefor NCS does not support this version?