Factory (RS3000) Alarm Complete Bypass or Removal Options

[Fastbird]

Ok, so in the process of the resurrection of our car, we're shaving the door handles, and moving up to an aftermarket alarm, most likely the Clifford Matrix RSX 3.3 as it has the amount of aux outputs necessary for operation of door solenoids and a trunk solenoid as well as remote start feature and even a turbo timer feature.

Our 99 is equipped with the Toyota RS3000 alarm system, and the ONLY stuff I can find is people talking about putting it in a car, not bypassing it in lieu of an aftermarket alarm system. So.......

Do I need to bypass the RS3000 alarm system, or can I leave it installed and not activated or unplug the module to ensure no accidental activation of the alarm. Has anyone here actually removed their factory alarm or bypassed it for another full aftermarket alarm?