I was able to get it working by adding
set interfaces ae0 ether-options ethernet-switch-profile tag-protocol-id 0x88a8
On my customer interfaces I did the following and seems to work fine.
set interfaces ge-1/0/0 flexible-vlan-tagging
set interfaces ge-1/0/0 native-vlan-id 3010
set interfaces ge-1/0/0 mtu 9216
set interfaces ge-1/0/0 encapsulation extended-vlan-bridge
set interfaces ge-1/0/0 unit 3010 vlan-id 3010
set interfaces ge-1/0/0 unit 3010 input-vlan-map push
set interfaces ge-1/0/0 unit 3010 output-vlan-map pop
However, if I try to create an interface with multiple VLANS I cannot pass traffic on either vlan-id
set interfaces xe-1/2/2 flexible-vlan-tagging
set interfaces xe-1/2/2 mtu 9216
set interfaces xe-1/2/2 encapsulation extended-vlan-bridge
set interfaces xe-1/2/2 unit 3010 vlan-id 3010
set interfaces xe-1/2/2 unit 3010 input-vlan-map push
set interfaces xe-1/2/2 unit 3010 output-vlan-map pop
set interfaces xe-1/2/2 unit 3016 vlan-id 3016
set interfaces xe-1/2/2 unit 3016 input-vlan-map push
set interfaces xe-1/2/2 unit 3016 output-vlan-map pop
Any ideas?