So I was able to get my buddies RPi3 running RetroPie 4.0.2 this weekend, and after configuring one PS3 gamepad on the RPi, plugging in the second PS3 via USB worked flawlessly! All the issues I read about must have been regarding older distro versions of RetroPie. I was also able to get both gamepads working on the onboard Bluetooth of the RPi3! Thank you for the help @obsidianspider and @Lyle_JP!
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