Flapsforty, answer to your question.
When the aircraft has stoped and the doors are OPEN the local authorites have control, ie if an incident takes place with a pax and you request assistance, or a law in the visiting country has been broken. Once the Doors have been CLOSED for takeoff, the commander has authority on behalf of the authorities of the contry the A/C is registered in. We had a canadian registered A/C a few years ago, and if there were any onboard incidents during flight theses were governed by canadian laws and not our UK ones. With regards to customes, yes it is courtesy for them to seek permission before boarding, however in almost all countries, customs officals have the right of entry and the right to detain the aircraft and its occupants without seeking permission from either the Airline, captain or local courts.
Hope this helps.