I've since figured out what was the issue with AU Aliens saved to the Character Pool not showing up during campaigns. It turns out that when they get saved to the character pool they don't get assigned the variable that enables them to be picked up by the game to spawn as soldiers. To fix it you must open the character in the Character Pool and uncheck and then recheck the Allowed Soldier box, if the alien has one.

The last bit is the tricky part, since some (if not all) of RealityMachina's species modules don't have their custom UICustomize_Menu set up with the character pool controls visible. For that reason, I've added a couple of console commands to this mod to manually check if that flag is set to true, as well as setting it to true allowing your aliens to start appearing.

• First, you can use ListCharPoolAllowedSoldierStatus [TemplateName] to list all characters of that type in the character pool and whether they are flagged to be allowed as soldiers or not. This command also prints out the same names to the log file, to make copy-pasting them easy. For example, you could use ListCharPoolAllowedSoldierStatus RM_HybridSoldier to list all Hybrids in your character pool and see which ones got the flag enabled.
  
• Then, for each of the soldiers that returned false in the list above you can use CharPoolSetAllowedSoldierToTrue [Soldier Name] to set their flag to true.

And voila, they should be showing up for your campaigns.

If you don't use this mod/don't wanna use this mod for its other functionalities, both commands can be run from the main menu. That means you can enable the mod, run the necessary commands to enable your character pool aliens, then disable it and relaunch the game without it with no harm done.