What does "Always Allow..." actually do? That is, what files does it actually change? I am deploying a new version of an application on to multiple machines (100+) and when I test it on a machine, the "You do not have permission to use the application" box pops up, due to quite strict restrictions on the machine. If I click "Always Allow..." then everything works fine. However I do not wish to have to click this box on 100+ machines. Is there a command line alternative which can accomplish the same thing?
If you can't work out what "Always Allow" does, I would suggest running something like fseventer to see what OS X changes. If it hits a plist file then you'll be able to run defaults on it. 

I'm assuming its probably in the com.apple.applicationaccess.plsit. (But not tested)