I have used House of Moto to upgrade from 4.1.2 to 4.4.2 last month.
My bootloader was unlocked previously and the phone was rooted as well.
After upgrading to 4.4.2, the bootloader warning disappeared and never came back. Samurai indicated that Motorola has changed something and so the warning no longer appears. I actually like this change.
The root - well I am not sure if it is still there, but as long as bootloader is unlocked I have control.