Correct, both vlan.x and irb.x virtual interfaces will show down until at least one of the physical interfaces associated with them are link up.
fxp0 cannot be used for any transit traffic as a port. This can only accept and originate management traffic. Typically we use this for the OOB address. This can get tricky because this interface lives in the base or root routing instance. So if you do have an OOB network and use the interface you may need to move your other interfaces into a virtual router routing instance to have independent default routes and prevent asymmetrical routing with management traffic.
In transparent mode you cannot do any routing. and all interfaces are in the same broadcast domain for layer 2. This is typically used to insert a firewall into a line without having to change any of the current network topology. So it sounds like you want to switch this back to layer 3 mode. This may also be the source of some of your errors.