In general, Beaglebone is more customizable so you will strip out what you don’t need. You will use the processing power to run your applications and not the OS, then you would need to focus on ensuring your OS is always up to date, more frequently using OTA updates to run the latest libraries. With Raspberry Pi with more processing power, you will need less control. So it comes back to the entry level being higher with Beaglebone. It requires more thinking and more preparation.
When Mender was started, Beaglebone was the only reference board for the Yocto Project so it is a good choice to run with this custom Linux distribution. On the other hand, if you want to use Yocto with a Raspberry Pi board you will need to use external Yocto layers. Raspberry support for Yocto is maintained by Balena. Yocto is not a go to solution when using Raspberry Pi, you will more likely go for the bundled and supported Raspbian OS as you will have all the support for the peripherals out of the box.
Both operating systems are supported by Beaglebone Black but you need to also check support for peripherals. For advanced features, you will need to add extra libraries. Beaglebone support for Debian and Ubuntu was not the case in the past as you needed a special Linux distribution called Angstrom Linux to operate a Beaglebone Black. The BeagleBone still comes preinstalled with a version of Angstrom. But Debian is frequently selected as the operating system: it is the distribution with the widest software support in embedded systems. To change the Linux distribution on the BeagleBone board, you will need some additional software and a microSD card reader. But be warned that the process can be labor-intensive requiring the user to download distributions compatible with the BeagleBone Board available to download from BeagleBone Latest Images . There is a full tutorial available here on how to install Debian successfully on the Beaglebone Black.
There is a dedicated tutorial to help you integrate Mender OTA software updates and the Yocto OS layer into a BeagleBone Black. Here is a tutorial on converting Debian to work with Mender and a Beaglebone Black.
Read these articles on Beaglebone Black in an embedded Linux project: