You can use a nsp forwarder for Retroarch.It doesn't break it, RetroArch just has an option to set CPU clock speeds and it is unable to if OCS is being used. You can set CPU manually using OCS but it'd be nice if it honored requests from other homebrew to change clocks.
Using RetroArch as an applet homebrew, you can't make an OCS profile for it, it will inherit the profile of any app ID that is overridden by atmosphere.
It'd also be nice if OCS didn't load app ID profiles if the app is overridden by homebrew, if that's possible.
To set different OCS profiles for different roms.