Hello,
The switch port to which the Root AP is connected should be configured as the trunk port for Ethernet bridging to work. Thus, you will be setting the RAP to Trunk as well
" What is the difference between VLAN trunking native and Native VLAN ID? Are both needed? "
- I believe the "VLAN trunking native" informs the native vlan of the wired backhaul to the RAP for untagged traffic over the LAN side.
- The "Native VLAN ID" in the ethernet port config portion is for specifying the VLANs to allow over the wireless backhaul so anything specified there will be allowed over the ethernet port and then over the wireless backhaul. This is typically mainly for the MAP which likely has a switch attached needing to pass traffic over the air but you need to enable both as trunk and then allow the VLANs needed on both side
This will more than likely be the same native vlan for both