Using neopo flash-all will flash application and DeviceOS exactly like Workbench does. IIRC neither Workbench or neopo will flash the bootloader however, and I think the boron is trying to download the bootloader from the cloud. (I should add a command to neopo for this.)
In the meantime, I think you can download the appropriate boron bootloader from the releases page and flash it to your boron with DFU.
EDIT:
@tunahammer I've pushed an update to neopo to provide a command for easily building and flashing the bootloader for a specified platform and Device OS version. Simply update your neopo installation and the new command will be available.
For example:
neopo bootloader boron 3.1.0
Also, you said you never activated your boron. Is it possible that you need to set the setup flag to done?