If the VPN client you use runs on a Windows PC, it sets up an L3 tunnel even though the protocol name is L2TP. Interfaces of L3 tunnels cannot be member ports of bridges. L2TP as such does support bridging, so you can set up an L2 VPN between two Mikrotiks using L2TP, but the PC client doesn’t.
To my knowledge, out of all VPN types supported by Mikrotik, only the OpenVPN client on Windows PC suppports bridge mode, but OpenVPN implementation on Mikrotik only supports TCP as transport which means some headache where packets get lost on the path between the client and the server.