GPO's are two part. The machine and the user. If they are applied to the machine, they use the system account. if they are applied to the user, they use the user account.
Curious, what change do you need to make on the machine? There are some tools that you can use to change permissions and apply that via a GPO Loginscript to the machine. We do this for installing our antiPest software. Had to write a little virus like script, but it works very well.
Also, best way to test GPO's is by creating a OU to contain the users/machines that you want to test on. They can be under the main OU, so that they still get upper level propigation, but you can apply other GPO's to them directly without effecting other machines/users outside the OU.
Good luck