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Thank you for contacting us.
I think this issue is more related to PX4, the best recommendation that we can give you is to contact PX4 to assist you in a better way. This is the link: https://github.com/PX4/Firmware.
Feel free to post the solution here, if you find the way to do this. It could be helpful for the community.
Have a nice day.
The error message
"ERROR [logger] failed creating log root dir: /fs/microsd/log"
Is more related to the way PX4 starts the logger. The microsd is connected by default to Aero, not the flight controller. Support for logging on Aero has been added recently to PX4 by using the UART between the flight controller and Aero to save the logs. This is available on the new version of the BSP (v1.2) and the logs should appear on /var/lib/mavlink-router automatically. This is how the logs available on logs.px4.io (search for "aero" in http://logs.px4.io/browse ) are generated.