I'm using NRF Connect SDK 2.1.0 and a 52840DK. In normal (non-bootloader) mode bluetooth initializes fine (bt_enable succeeds). However, when I start using MCUBoot, bt_enable fails, apparently because bluetooth settings (CONFIG_BT_SETTINGS) doesn't detect NVS.
This all used to work fine when I was doing everything by hand from the command line, so it may have something to do with switching to NRF Connect. However, I also changed zephyr versions at the same time so it's hard to say for sure.
EDIT: I should also note that I'm using NRF Connect for VS Code, which seems a little twitchy at times. I don't know if the build generation step is doing something to mess with this but it seems to be working correctly. I'm using a MCUBoot overlay conf to patch in a key, etc. but other than that should be straightforward.