HPTuners is a device/software that allows you to reprogram things on the PCM. It'* similar to the dealers Tech2.
It depends on what the anti-theft system is setup to do. On some cars, it disables the fuel injectors, or it disables the fuel pump, or it will disable the starter.
And no, you cannot just simply "bypass" the system. It'* much more elaborate than just snipping a wire, or whatever.