Okay, if I was you I would have a look at the map file and try to figure out what it's putting there and why.
From: Jamie Mccrae <Jamie.Mccrae@lairdconnect.com>
Sent: Thursday, April 4, 2019 2:34 PM
To: Bøe, Sebastian; email@example.com
Subject: RE: Removing padding from generated hex files
I have tried that but it still pads the first section with 0x00 bytes. I'm using a custom board file and project so tried switched to trying it with the hello world sample using the nrf52840_pca10059 board file and enabled the option there, the area where the MBR is, is filled with 0x00 inside the hex file.
IMHO this should be the default. Needing to fill the gaps is indicative of a problem
elsewhere, e.g. in the linker scripts.