Something is definitely very wrong in your environment. The fact that it is not picking up the App Home and including it in the psadmin -envsummary output, is concerning. i.e: I would expect to see a file system location for PS_APP_HOME also echoed. I thought that the PS_APP_HOME location was always set via the psadm2 user's profile.
I don't know what to suggest at this point. You could of course try resetting the VM and then doing a fresh boot of it. If you want to try this out here is what you would do:
(as root)
(1) Invoke the command /usr/sbin/oraclevm-template --cleanup
(2) Invoke the command /usr/sbin/oraclevm-template --enable
(3) Reboot the VM
(4) When the VM console comes up go through the initialization prompts and make sure that what you're prompted matches what is described in the PUM manual that accompanied the PUM download on MyOracleSupport.
If you're still seeing the issue then I'd probably want to ask you for some more info. It's kinda hard when I can't see the machine, y'know.