users will still have to tell if they want to launch the ISO from USB or SD if they have both of them.
some loaders allow listing of the device one by one, but USBloaderGX for example list all devices at the same time and skip duplicates automatically based on detected MIOS type.
If DIOS MIOS Lite is installed in MIOS slot, it will list SD card in priority, and display non already present games USB dump with a warning "You need to copy on SD first".
If DIOS MIOS is installed in MIOS slot, it will list USB in priority.
There's a way to force SD or USB only, but I don't know if users are aware of that option.
The loader can't decide if you want to launch DM or DML if you have the iso in both devices.
A new (and maybe confusing) "default boot device" setting would be needed.
But it's the loader's problem. If Maxternal can make multiple MIOS Slot he doesn't have to care about the future user's decision.