meta-oryx system profile settings override user layer settings.
I'm unsure of the solution here, but let me explain what is happening.
Because native/guest are hardcoded in some places and we have to carry those conf files with those names, we are carrying in our distro layer our own native.conf/guest.conf. The issue is, the meta-oryx native/guest.confs seem to be overriding some of our settings in those files.
Interestingly enough, BB_LAYER_PRIORITY doesn't seem to fix this behaviour. So, my stopgap here is to rm those two files.
This might just be PEBKAC or a documentation issue.