Refer to Exhibit.

The trunk still forms with mismatched native VLANs and the traffic can actually flow between mismatched switches. But it is absolutely necessary that the native VLANs on both ends of a trunk link match; otherwise a native VLAN mismatch occurs, causing the two VLANs to effectively merge.

For example with the above configuration, SW1 would send untagged frames for VLAN 999. SW2 receives them but would think they are for VLAN 99 so we can say these two VLANs are merged.