Turns out it still doesn't work ! :(
I thought it did since I used the alternate line AFTER I changed the shader using the Retroarch GUI. Now even if I delete the new line or change it, no change to the shader :(
Somehow, changing the shader through the Retroarch GUI does it, whatever is in the retroarch.cfg file.
Now what I'm thinking, could it be something to do with file permissions ? That shader line, does it tell the system to change another file properties and maybe it isn't able to do it because of file permission ?
I am thinking about this since I see other posts about file permission issues, requiring to do something like :
Sudo chown pi:pi /opt/retropie/configs/
Could that help ??? At work right now...