With mender-convert, the kernel*.img file is actually U-Boot which then loads the kernel from the active root filesystem. You probably need to put your updated kernel in the /boot directory of each of the root filesystem partitions.
That makes a whole lot of sense, that way the filesystem update can contain a new kernel.
Unfortunately, even if I replace both rootfs partitions /boot/zImage with my custom kernel, and leave the boot partition image unchanged from what mender-convert generates, I don’t get a working boot. I’m not sure where to look next because there is no output despite a loglevel=7 after the bootloader, just black screen.