So, what's the bottom line here? I don't think the development platform recommended by Nordic for the nRF52840 (SEGGER Embedded Studio with the nRF5 SDK) is usable for serious development. For sure, you can use it, but you're making life significantly more difficult for yourself than it needs to be. (For all the grubby details and the evidence to back up this claim, you'll need to read through the SEGGER Embedded Studio + nRF5 SDK notes.)
Most of the problems are with the nRF5 SDK. The SEGGER IDE is OK, as these things go, if not great. But those SDK problems are really hard to deal with. We need something better.
For what they're worth, here are my recommendations:
For application development, use Zephyr, ideally via PlatformIO. It really does seem to be the wave of the future, and peripheral and platform coverage and documentation are only going to get better.
The combination of using the Linux devicetree system and Kconfig is
very good. It makes it very clear what hardware resources are exposed
via operating system APIs, and it makes it very easy to configure the
use of different subsystems and libraries. The difference between this
setup and the unholy mess that is the
sdk_config.h file for the nRF5
SDK is really stark. Zephyr shows how these things should be done.
The kernel APIs in Zephyr are different from other platforms (they're not POSIX, they're not like FreeRTOS or any other RTOS), but they're easy to learn, and they're laid out quite logically. The APIs for more complex subsystems (e.g. Bluetooth) also seem quite logical, and in particular, the Bluetooth API has a nice combination of usability and access to protocol details needed for more complex applications.
(You can see the details of the development of the example programs using PlatformIO and Zephyr in the PlatformIO + Zephyr notes.)
For board bring-up, if your platform fulfils the requirements to get CircuitPython going on it, do your EEs a favour and use it! It's incredibly easy to use and it makes it extremely convenient to write little test programs to exercise different bits of functionality.
(You can see the details of my experiments with CircuitPython in the CircuitPython notes.)
That "fulfils the requirements" thing might require a little effort though. You'll need a friendly programmer to set up a custom board support package for your board and build a custom CircuitPython distribution. This is particularly important for the nRF52840, since more or less every pin is remappable.
I've not tried this, but it looks as though it ought not to be too hard. For example, if you take a look at the board definition for the nRF52840 development kit, it seems that more or less all you need to set up is the pinmux definitions for your board, plus a bit of boilerplate. You do need to have a board that supports USB, since CircuitPython relies on setting the device up as a USB mass storage device. (The USB pins on the nRF52840 aren't remappable, so they don't appear in the CircuitPython pinmux definitions.) So you write the custom board definition, build a custom CircuitPython distribution and install it onto your board. (You'd probably need to flash the Nordic bootloader first to get the necessary USB support going.)
The nRF52840 is a good MCU, but the nRF5 SDK slightly spoils the experience of using it. It's good to know that there are (much) better options available: Zephyr for application development and CircuitPython for experimentation and hardware development support (that's what I'd use them for anyway).