This would be possible to achieve if you were willing to split it into a couple of steps. If you wanted to apply definition queries to a map before opening you could do the following:
Firstly have a step that runs a python script (LaunchGP), which can utilise arcpy.mapping to manipulate the layers within the map - including adding a definition query to a layer. You could then either resave the map document or save it as a new map with the job number. Note that you can pass tokens through to the python script.
Then you can have a second step which launches the newly saved map document with the definition queries applied (LaunchArcMap).