What happens if a Cisco trunk mode port has an access VLAN and a native VLAN that are different?

Ignorant question here, but I'm coming from the HP and Brocade world. I'm looking at a Cisco port. It's in trunk mode with a set of VLANs allowed on the trunk. The Access Mode VLAN is 1, and the Trunking Native Mode VLAN is 99.

Does the Trunking Native Mode VLAN setting take precedence for untagged traffic since the port is in trunking mode, and the access VLAN setting doesn't get used at all? Otherwise this looks like two untagged VLANs at the same time.