I have had a similar requirement very recently, whereby i worked around it by creating a custom image bbclass recipe to produce a 2nd rootfs ext4 with some things removed.
I recently supplied a pull-request upstream which will be merged soon, that allows you to set the name of the ext4 image that mender-artifact uses to create the mender file via a bitbake variable in local.conf.
combining these two things i was able to have a factory image and .mender image created from different ext4 files
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