I have exactly the same question.
I did find out that it's possible to add another unit to the uplink port, with a single vlan, in your example that would be:
set interfaces ae2 unit 1 vlan-id 900
That works for a single vlan, but not for a list (adding 100 units with 1 vlan would be a bit weird i guess)
Also other layer2 stuff like for example spanning tree does not seem to be working anymore on the uplink port (probably because there is no family ethernet switching anymore?)
Did you find a solution for your problem?
Shouldn't it be possible to create a trunk port which trunks both single and double tagged vlans? And still keep the layer 2 stuff like spanning tree working?