Hi @VolcanicCheese
Thanks for your reply!
If you have the boot pins set to 00 and you want to avoid entering to serial downloader mode you will have to burn BT_FUSE_SEL as 1. Then, specify the boot config to boot from your memory option. That way you can boot from your external flash.
As you mention, the MCU boot utility will let you do this. Here is an snapshot showing the boot config 1 with the BT_FUSE_SEL.

Our colleague who made the utility gives a quick overview on the github page.
Also, with this you should be able to debug your application as expected. However the inconvenient that I can see is that if BT_FUSE_SEL is burned, you won't be able to enter serial downloader mode again.
The serial downloader mode can be used to regain debug access during development process. As a problematic image, that crashes the MCU, can be prevented from running be replaced by a good one. That is a reason why fuse burning is recommend for production stage.
Regarding the watchdog : I do not see any problem. You are using the same flash memory that the 1020 EVK uses a default boot option.
Let me know if you are still having inquiries that we could address.
Diego