Thanks for the advice.
In my trial using 2 images, I have the following:
- first image generates a rootfs + other partitions (/var) in wanted format (squashfs+verity & ext4). I delete content of /boot as it will be generated by the second image
- second image is a really simplified version to just compile u-boot, bootscript, kernel-base and fitimage and generate /boot as a ext4 partition
Second point is that UBOOT_ENV can only be set at machine level. So I need an empty bootscript for the first image as I can't disable fitimage generation depending on image variant (even by removing do_assemble_fitimage manually)