but im confusing because i can assign different vlan for each port , and assign all these Vlans in the bridge domain ::
>> is that means that these vlans will be able to communicate with each other ???
Yes, that is one usage of a bridge domain. This is more common on the MX than the SRX.
An example might be multiple trunk ports bringing vlans to the MX. these naturally have different tags as they share a trunk port to arrive on the MX. But they come from remote services on the network that are actually in the same broadcast domain.
The bridge domain on the MX contains all of the sub-interfaces with different tags. And bridges these vlans into the same broadcast domain so they can communication layer 2.
Now with transparent mode on the SRX we have a different case. Here there can ONLY be a single broadcast domain that is layer 2 transparent to devices outside the SRX. All interfaces on the SRX in use are put into the bridge domain so they can communicate.
The IRB interface becomes the mgmt address for the SRX.
And zones are by physical interface so that security policy can be enforced for traffic that remains layer 2 throughout the SRX.