WRT Question 1
In balenaOS the
/mnt/boot is the place where the boot partition is mounted. So please try placing the overlays under that folder.
WRT Question 2 (continued)
We are using yocto for building balenaOS, so the best way to customize it is by using yocto as well.
We do not have a guide for this, but you can find some references in
WRT Question 3
Most device wifi chips only support either being connected on a wifi network or being on hotspot mode.
Which WiFi adapter are you using?
WRT Question 4
Unfortunately we do not support the BBB networking over USB feature currently.
On the other hand this sounds interesting & useful, so I will open an internal issue to add this to the list of features to consider.
WRT Question 5
BalenaOS as a host operating system is keeping OS related logs in memory and systemd preserve the most recent ones that do fit in their max specified log size.
On the other hand, if you need to preserve application level logs, then your application also has to handle log preservation & rotation.