As far as I know the GEM (Generic Electronic Module) controls multiple functions: wipers, window switches, convertible top, airbag power, datalink, etc. You may loose the ability to communicate via an OBDII connection. There should be a fuse in the power junction under hood that you can pull that kills the GEM an check for engine functionality. Fuse number 7 I believe, GEM/interior lights.
I don't think the relation ship between it and the PCM is important for starting and running , only for communication of the OBDII diagnostics.