“Trunk with native VLAN” in Cisco is “hybrid” in Mikrotik. So configure port to: “vlan receive - any” and set “default vlan id” to “native VLAN ID” of your choice (e.g. 4000). You have to mark such port as member of VLAN with “native VLAN ID” (e.g. 4000). In mikrotik “native VLAN” is not setup any different than the rest of VLANs.