I just installed the Beta 3 and the settings for the splashscreens appears to have changed. It used to be in /home/pi/RetroPie-Setup/supplementary/asplashscreen/asplashscreen but that does not exist anymore.
The settings are stored in /etc/splashscreen.list – the file you mention is the init.d script for launching the splashscreen. If you need to customise that it has moved to scriptmodules/supplementary/splashscreen/asplashscreen
If you need details like this you can reference the changes on github
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