There are a few differences when adding VLANs in Transparent mode compared to NAT/Route mode.

In Transparent mode, VLAN traffic is trunked across the VDOM. That means VLAN traffic cannot be routed, changed, or inspected. For this reason when you assign a VLAN to a Transparent mode VDOM, you will see the Addressing Mode section of the interface configuration disappear in from the web-based manager. It is because with no routing, inspection, or any activities able to be performed on VLAN traffic the VDOM simply re-broadcasts the VLAN traffic. This requires no addressing.

Also any routing related features such as or Virtual Router Redundancy Protocol (VRRP) are not available in Transparent mode for any interfaces.