The equivalent of the "native vlan" on the SSG would be configuring the ethernet interface without creating a sub-if.
From your config:
set interface "ethernet3/1.1" tag 540 zone "OOB-3560"
set interface "ethernet3/1.2" tag 900 zone "HSGR-ADMS-OOB"
...
set interface ethernet3/1.1 ip 172.21.59.65/28
set interface ethernet3/1.1 route
set interface ethernet3/1.2 ip 192.168.202.20/24
set interface ethernet3/1.2 route
You have VLAN 540 tagged on eth3/1.1, and 900 tagged on eth3/1.2. Let's say you had VLAN 400 configured on your Cisco for the 172.10.10.0/24 network as an example -- your Cisco config might look something like this:
interface Vlan540
ip address 172.21.59.66 255.255.255.240
!
interface Vlan400
ip address 172.10.10.1 255.255.255.0
!
...
interface GigabitEthernet0/49
switchport trunk encapsulation dot1q
switchport trunk native vlan 400
switchport trunk allowed vlan 400,540,900
switchport mode trunk
!
That would send your 540 and 900 VLANs tagged with 802.1Q frames, and your 400 VLAN untagged to interface eth3/1 on your SSG. On the SSG side, you would just configure ethernet 3/1 like so:
set interface ethernet3/1 ip 172.10.10.2/24
set interface ethernet3/1 route
Since the frames are untagged, you don't have to configure a sub-if or VLAN tag.