Based on the last few updates I could corner the isssue just to virt-aa-helper.
There is no active instance of libvirt involved which hopefully eases the 
debugging.

Here what I just sent to upstream: https://www.redhat.com/archives
/libvir-list/2017-July/msg00627.html

I was mislead by my former assumption on the lifecycle.
As virt-aa-helper gets his xml passed into stdin.
I captured that and found that in both cases it had the same content.
Below steps to reproduce based on that:

Test -Xml:
<domain type='kvm' id='1'>
        <name>kvmguest-artful-normal-a2</name>
        <uuid>f4239a92-f933-4bd3-b9fb-b9c260a7dc65</uuid>
        <memory unit='KiB'>524288</memory>
        <vcpu placement='static'>1</vcpu>
        <os>
                <type arch='ppc64le' machine='pseries-zesty'>hvm</type>
                <boot dev='hd'/>
        </os>
        <devices>
                <emulator>/usr/bin/kvm</emulator>
                <disk type='file' device='disk'>
                        <driver name='qemu' type='qcow2'/>
                        <source 
file='/var/lib/uvtool/libvirt/images/kvmguest-artful-normal-a2.qcow'/>
                        <backingStore/>
                        <target dev='vda' bus='virtio'/>
                        <address type='pci' domain='0x0000' bus='0x00' 
slot='0x03' function='0x0'/>
                </disk>
        </devices>
        <seclabel type='dynamic' model='apparmor' relabel='yes'>
                <label>libvirt-f4239a92-f933-4bd3-b9fb-b9c260a7dc65</label>
                
<imagelabel>libvirt-f4239a92-f933-4bd3-b9fb-b9c260a7dc65</imagelabel>
        </seclabel>
</domain>


File:
qemu-img info /var/lib/uvtool/libvirt/images/kvmguest-artful-normal-a2.qcow
image: /var/lib/uvtool/libvirt/images/kvmguest-artful-normal-a2.qcow
file format: qcow2
virtual size: 8.0G (8589934592 bytes)
disk size: 200M
cluster_size: 65536
backing file: 
/var/lib/uvtool/libvirt/images/x-uvt-b64-Y29tLnVidW50dS5jbG91ZC5kYWlseTpzZXJ2ZXI6MTcuMTA6cHBjNjRlbCAyMDE3MDcxNg==
backing file format: qcow2
Format specific information:
    compat: 0.10
    refcount bits: 1
    
To be sure I undefined the guest to not have "a different source" or 
information.

Generate a new profile:
$ /usr/lib/libvirt/virt-aa-helper --create --dryrun --uuid 
'libvirt-f4239a92-f933-4bd3-b9fb-b9c260a7dc65' < test-virt-aa-helper.xml

In 3.5 this is no more having the line:
/var/lib/uvtool/libvirt/images/x-uvt-b64-Y29tLnVidW50dS5jbG91ZC5kYWlseTpzZXJ2ZXI6MTcuMTA6cHBjNjRlbCAyMDE3MDcxNg==

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https://bugs.launchpad.net/bugs/1704782

Title:
  qcow base image apparmor rule missing in artful

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