Would it make much difference if it wasn't?

The worst that could happen is that you couln't switch the alarm on, as inserting the key into the ignition and switching it on automatically switches off the alarm.
Alternatively you can do away with the alarm fob altogether. Just set the alarm to come on automatically when the ignition is switched off. Then when you return to the bike you switch off the alarm as above i.e. insert the key and switch on the ignition.
Peter