I'm not sure which active/boot flag you talk about.
The Kobo exports the filesystem directly as a block device, without an additional partition table. In Linux that means you mount /dev/sdx,
not /dev/sdx1 (sdx being the entire block device, sdx1 would be a partition that does not exist in the case of Kobo).
So is there a boot flag or whatever as a property of the filesystem itself?
If we could understand this issue better maybe it would be possible to mod the firmware / tell Kobo about it so in future firmwares this issue never comes up in the first place.