I remember a topic a month ago with a similar problem - the pairing of Xbox controllers worked, but they acted as a single controller. The solution was to install an alternate driver for the controller - xpadneo (https://github.com/atar-axis/xpadneo).
If you want to give it a try, the installation is quite easy:

Remove any Bluetooth controller from the RetroPie script Bluetooth configuration. Remove the xpad driver from the RetroPie setup script, from the drivers package section. Install xpadneo (run this from the SSH session): git clone https://github.com/atar-axis/xpadneo.git cd xpadneo sudo ./install Reboot and then redo the Bluetooth pairing for the controllers.

See if you get 3 devices (/dev/input/event[0-2]) and Emulationstation detects all your controllers after the installation.

I have a similar controller (mine is red and black). I wouldn't say it is automatic compatible. I configured for retropie months (a year?) ago, and as I remember I had to restart the bluetooth registering procedure several times until the controller was recognized by the Pi3.
After that it was OK for me. Well, I had some issues with vice (C64), but when I figured it out and fixed it (my mistake) I could - and I'm still able with the latest Pi - play with my C64 games.
Emulationstation menu is also ok.
And the twist:
a couple of days ago I wanted to try out some other games (PSX, and gamesandwatch) and it seems that there are some mapping issues. I can't find the reason, I guess it is just again some configuration glitch... Still investigating.

I don't have any idea what this might be. I use an iBuffalo SNES-style controller, and think it's great. No problems at all configuring the controller or using it with any of my games...