The abduction tuning isn't an issue anymore. I've updated that on my end and that file is identical between the both of us. So no matter whose tuning loads you'll see the correct intended outcomes.
v4.0 did add two new conflicting files, which are there recipes for Alien Juice and Space Energy. UFO Investigator makes it so that the Alien Guru trait will unlock these recipes. Aliens Reloaded makes them available to generation one full aliens (ie, they were born on Sixam and learned it there) and those with Alien Lore 5 or higher.
I've added support for the Alien Guru trait to both of these recipes as well (you can be in the required careers, a full gen one alien, have high enough Alien Lore, or be an Alien Guru to unlock them), but I don't believe Ilkavelle has had time to update UFO Investigator for compatibility / might not be aware that AR has been updated. So depending on whose mod loads first the recipes may be inconsistently available.