Ok. I just re checked the ignition key barrel.
When you turn it to ignition/run there is power coming from the key barrel. I then turned the key to start it. There was still power coming from the ignition wire.
Therefore during start/crank there will be 12v coming from the barrel through the ballast resistor through the junction up to the coil which then turns into 5v at the coil. at the same time 12v comes from the starter to the junction.
5v meets 12v on the same line. This is the way Escorts work during crank/start.
I'm feeling the 12v coming from the starter solenoid is backtracking down the resistor to the alarm whilst at the same time 12v is running from the barrel to the alarm.
This is new technology meeting old.
So maybe this is seen as a "hotwire" which is why everything starts going funny.