@Clyde, this is a co-workers unit and he couldn't remember all of the details about it but I think that you are correct about it being a non official retropie image. It had a very out-dated version and when I updated everything is where the issue happened. I will talk with him at work Monday, explain what happened and let him know that I will set him up with an official copy.
Yes, I did what you said and I succeeded to lower boot time to 11 seconds for libretro emulator but only through autostart.sh.
However, non-libretro emulators still starts about 5 seconds faster through the rc.local script and I dont know what else I could do here.
It seems runcommand is a problem, because for some reason it refuses to start through rc.local properly...
I had RetroPie running on Mint for a short time and I didn't need to mess with the fullscreen options. All I did was add a startup delay of 3 seconds to the RetroPie entry. This stopped the issue. I would leave it as fullscreen and try that? I think this happens because if ES starts before X is running it doesn't launch. Not sure though but a slight delay should resolve.