The alarm system has several sections.
When you unlock the car with the fob you unlock the doors, switch off the alarm and switch of the starter immobilisation.
The car will remain unlocked and unarmed in some versions while other versions may relock the car and reset the alarm if a door isn't opened. The immobiliser normally switches off when the alarm is switched off but some models have a transponder in the fob that needs to be close to the ignition barrel to switch off the immobiliser.
Also the immobiliser will switch back on after the engine has been run.
The flashing light by the speedo shows that the immobiliser is in operation and the engine can not be started.
There are two main triggers for the alarm, voltage sensing primarily triggered by opening a door or the bonnet and in some cases a microwave sensor fitted behind the t bar in some models.
To avoid the alarm sounding but to otherwise secure the car lock it with the key in the key hole in the door, this will lock the doors and activate the immobiliser but will not set the voltage trigger or the microwave sensor. This should work on a ferry and I believe should apply to any car with remote locking.
Home to black Alfa Romeo 159 3.2 V6 Q4 ,green MGF VVC and red MG Maestro T16.
MG - the friendly marque.