Update: I've found the appropriate location tags here:
I now have jerboas spawning in the DinoSpawnEntries_CityCenter_C as well as Ext_DinoSpawnEntries_DesertOasis_C, and shadowmanes spawning nearby in DinoSpawnEntries_CityCenter_DangerClose_C. For anyone interested, the shadowmanes do go to sleep and you can harvest corrupted wood from gacha crystals on Extinction. It will just require unlocking the fish basket engram either by hopping arks or auto unlocking engrams to tame them. I haven't made it over to the cave yet to see if the desmodus are spawning properly.
Unfortunately, the ichthyornis are back and I don't know why. I added this line:
But it doesn't seem to be working