Hi there,
I just started using Embedded Studio (v5.10d on Windows 10, nRF Connect SDK version 1.4) with nRF52840dongle and nRF5340 PDK. Here is what I did
1. Copied nRF Connect SDK project from the original location to my own folder. Let's say it is blinky project from zephyr samples.
2. Run menu command "Open nRF Connect SDK project" for this new location. Selected either nrf52840dongle_nrf52840 or nrf5340pdk_nrf5340_cpuapp, makes no difference.
3. After a while project ES is created, but there is no entry where Options are enabled. I discovered when I tried to make changes recommented for dongle. Here is how project tree looks like

4. When built with defaults, blinky works on nRF5340, I see LED blinking. It doesn't work in case of dongle, not sure what defaults are in this case, because I don't see project options.
5. The only case when I see different picture is for the project peripheral_uart, here additional node is created and there are options enabled:

This project is not supported for dongle, so I cannot tell how recommended adaptation works. This was the only project that creates merged.hex.
I tried a number of different projects both from SDK and zephyr samples with the same result as for blinky one. I did software update today.
Am I missing something obvious? I just started with all this so it is very possible.
Thanks,
Sergei