It may not work as a PACKAGE until after the reboot ... you could start playing with just executing the raw command-line to consume your .REG file (as that doesn't use the "full" EPM agent, but rather relies on Provisioning bits).
You can combine that with a "RUNAS" type tool, if need be? It's a bit clunky, but if you have to do it at a certain piont in time & can't do the reboots before, then that may be an additional option for you?