For the Focus I keep the keys well away from the front door, as the MK2.5 ST is rapidly becoming one of the most stolen. Sadly that isn't a perfect solution as the OBDII port can for some stupid reason have another key programmed to it, which is the latest tactic from thieves.
JLR have half got there with the keyless system in that the ECU can only have two keys programmed to it at any one time, but that's of no help if the thief manages to replicate the signal.
I just used to pull the OBD2 fuse out in my ST.
Another trick is using a dummy port and routing the real one somewhere hidden. For some reason Ford like to have a huge blind spot at the front of the car which the alarm system can't see, along with no glass break detectors. They can break the window and plug something in without even setting the alarm off :/
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