These are the steps I’ve found to sequence root certificates into your AppV5 application.
certmgr.exe -add AddTrustCert.cer -s -r localMachine root
Where do you get certmgr.exe from?
The visual studio downloads apparently contains this tool.
Once you’ve started your sequencer and run the command it will add the certificate to these two places:
And that’s how you add certificates to a sequenced package.