I'm not sure I follow the question. But I think you are asking if you can control where traps are sent from on the device.
When you create the community, you can choose the source interface that your snmp traps for this community will use as the source to send from. Using this parameter you would select the interface that is included in the vpn tunnel to the trap server receiver in your case to get the traffic flow you desire.
Configuration > Report Settings > SNMP > Community
Set the source interface parameter