I've never run DU on an AGA machine. On my set-up, all of the available screen modes (NTSC and Picasso) show up in the Screen mode prefs menu. The fact that it runs in retargetable graphic modes makes it easier on the eyes than Distant Suns (still fun). It's hard to imagine it will not run in AGA modes.
This is one of my all time favorite programs and not a port from another platform, it utilizes the system resources well.
Glad to see someone else finding it. Did you buy it used or from the author?