Delta apply fail with "xdelta3: target window checksum mismatch: XD3_INVALID_INPUT"

Gave it a go my self, and indeed I can reproduce your problems. But to me it looks like mount changes something, e.g

root@qemux86-64:~# sha256sum /dev/hda2 /dev/hda3 
54eea8451754947be8f41d2ed3470dc63c8a599ed884b5a3938a96ea0f441b84  /dev/hda2

# Here /dev/hda3 has the expected value (same as in Mender Artifact)
852c1a0e9e36488d4c7746b5857d309037ad8f43185ee2ab81c7bec07dd69c11  /dev/hda3
root@qemux86-64:~# mount -o ro /dev/hda3 /mnt/
[  130.417154] EXT4-fs (hda3): mounted filesystem with ordered data mode. Opts: (null)
root@qemux86-64:~# sha256sum /dev/hda2 /dev/hda3 
54eea8451754947be8f41d2ed3470dc63c8a599ed884b5a3938a96ea0f441b84  /dev/hda2

# Here /dev/hda3 changed just after running the mount command
54eea8451754947be8f41d2ed3470dc63c8a599ed884b5a3938a96ea0f441b84  /dev/hda3

So I would suspect an ext4 feature is causing this.