The E164 settings in the trunk are for incoming calls to modify the number calling in.
The global E164 settings of the PBX are there to modify an international format number into your local format. Sometimes local providers do not accept local numbers in international format.
So something that might be useless for you because your provider is OK with that, might be helpful for someone in another country because their provider doesnt.
We have to cater for all eventualities.
Lets see an example of E164. (I put Switzerland which is local to you. Everyone else, adjust accordingly to your own countries and regions)
In this example if a user dials someone in Zurich who is in the 043 area code dials +41431234567 the PBX will dial just the number 1234567 which is the local portion of the number.
If they dial 043 the PBX will again just send out 1234567. This is because we have Remove if same country and remove if same area code selected.
Now...
If we dial someone in Zurich in the 044 area code, the PBX will dial 0431234567 because our PBX is configured in the 043 area code.
And just as an FYI, in telephony, the 0 is a NATIONAL PREFIX. It is NOT part of the area code, eventhough over the years it is referred to as part of the area code.