I am not really sure what to recommend here, as I have never been in a situation where I run docker on a machine with limited memory, or on external drives. Both alone have potential for causing the trouble you experience. I used an alternate data-root directory in the past without any issues, so that’s less likely to be the problem.
We had a post recently about nginx not restarting after the machine was rebooted (See: topic), but no solution was found. Since baikal seem to base on the nginx image, it could be related.