I was wondering if the box was finding an older /storage partition from the older install, but blkid shows none of the partitions that exist on eMMC have partition GUIDs or names that would match so that's a dead end. And I meant "ssh" before, so that's not an issue.
You did mention running a custom OS and not the stock one, but I don't really see how that could impact on Linux since the box is still booting (vendor u-boot) and hooking it to boot LE from SD card. Both stock and current OS are likely to use the same u-boot code.
There's a pattern where services are waiting for things on the SD card second partition (/storage) to become available which results in some messages in the journal log, and the overall speed of boot looks a little slow to me. However I'm used to looking at logs from devices that boot from faster eMMC so that's just perception, and my boot logs also show similar messages: and ultimately /storage does mount and things do continue. I can't explain why the sshd.conf file hasn't been created automatically, but perhaps related to the second-boot failure to mount the storage partition. However boot scripts should still detect its absence on third boot and create that conf; it's not a one-time/first-boot only thing.
In short, I'm a little stumped 