Got it working, if anyone else is interested in using this bezel pack, I combined the bezel and crt overlays for each game into one image using gimp, exported that as mslug.png and then I made a .cfg file and named that mslug.cfg . Put both files in the opt/retropie/emulators/retroarch/overlays folder. Make sure you name both the .png and .cfg files the same for each game.
I'm going to assume you're using lr-gambatte as your GB emulator.
Start a GB game.
Open the RGUI by using the hotkey combo you have setup (by default: Select + X)
Scroll down to Options and press A.
Scroll down to GB Colorization
Press left or right to cycle through the options from Custom to OFF.
Press B to exit to the Quick Menu.
Scroll to the top to Resume.
Press A on Resume to resume the game.
The green overlay is now gone. Feel free to try out the different colour modes and see how they look.
@Clyde That would be awesome. I've written a script that will take a folder of videos and, using FFmpeg, overlay images on top of them like scan lines and a bezel and spit out a new video. It would be so nice to be able to do this as an image instead like retroarch does.