I appears that it's not possible to sign the appx package using a cert from your local cert store or from a USB token.
I think this would be easy to fix. I suggest adding a config param called devCertSha1. If this is set, then instead of doing
signtool sign -f <program.devCert> -fd SHA256 -v <appxFile>
the app would do
signtool sign -sha1 <program.devCertSha1> -fd SHA256 -v <appxFile>
If this sounds reasonable, I'll make the changes, test it, and put in a pull reqeust.