I'm surprised this one took me so long!
Select Rex, don't worry about loadout, the ability you need for this (DIRECTIVE: Disperse) is the only utility option at the moment, and enter the level. Abandoned Aqueduct is one of the Second Stages, so you need to run the first stage and enter the next level. You can use the Newt Alter and head to the Bazaar Between Time and see if you can buy a TP to the Abandoned Aqueduct, but I don't find that this guarantees Aqueduct.
Once you're at Abandoned Aqueduct, play through the level and activate the Teleporter when you're ready. Clay Dunestriders are more common on this level, but not a guarantee, so you may need to run this a couple of times. Next, get the Dunestrider's attention and lead it to the big pit at the open area of the level; keep running over the bridge and try to draw the Dunestrider as close as possible to the edge of the pit. Once you're comfortable with where it's standing, run over to it, position yourself with the dunestrider between you and the pit, and use DIRECTIVE: Disperse. This may take a couple of attempts, but it should be easy enough!