Been looking into routing-instances and going to try something like this later today and see if that separates the traffic:
set vlans TEST-VLAN vlan-id 50
set interfaces ge-0/0/1 description "STORE-A TRUNK"
set interfaces ge-0/0/1 unit 0 family ethernet-switching port-mode trunk
set interfaces ge-0/0/1 unit 0 family ethernet-switching vlan members TEST-VLAN
set interfaces ge-0/0/2 description "STORE-B TRUNK"
set interfaces ge-0/0/2 unit 0 family ethernet-switching port-mode trunk
set interfaces ge-0/0/2 unit 0 family ethernet-switching vlan members TEST-VLAN
set interfaces ge-0/0/3 description "STORE-A ACCESS 1"
set interfaces ge-0/0/3 unit 0 family ethernet-switching port-mode access
set interfaces ge-0/0/3 unit 0 family ethernet-switching vlan members TEST-VLAN
set interfaces ge-0/0/4 description "STORE-A ACCESS 2"
set interfaces ge-0/0/4 unit 0 family ethernet-switching port-mode access
set interfaces ge-0/0/4 unit 0 family ethernet-switching vlan members TEST-VLAN
set interfaces ge-0/0/5 description "STORE-B ACCESS 1"
set interfaces ge-0/0/5 unit 0 family ethernet-switching port-mode access
set interfaces ge-0/0/5 unit 0 family ethernet-switching vlan members TEST-VLAN
set interfaces ge-0/0/6 description "STORE-B ACCESS 2"
set interfaces ge-0/0/6 unit 0 family ethernet-switching port-mode access
set interfaces ge-0/0/6 unit 0 family ethernet-switching vlan members TEST-VLAN
set routing-instances STORE-A description "Store A routing-instance"
set routing-instances STORE-A instance-type l2vpn
set routing-instances STORE-A interface ge-0/0/1.0
set routing-instances STORE-A interface ge-0/0/3.0
set routing-instances STORE-A interface ge-0/0/4.0
set routing-instances STORE-A route-distinguisher 1234:1
set routing-instances STORE-A vrf-target target:1234:1
set routing-instances STORE-B description "Store B routing-instance"
set routing-instances STORE-B instance-type l2vpn
set routing-instances STORE-B interface ge-0/0/2.0
set routing-instances STORE-B interface ge-0/0/5.0
set routing-instances STORE-B interface ge-0/0/6.0
set routing-instances STORE-B route-distinguisher 1234:2
set routing-instances STORE-B vrf-target target:1234:2