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 dynamic routing or Virtual Router Redundancy Protocol (VRRP) are not available in Transparent mode for any interfaces.