UPDATE!
There IS a way to get it to work but it's very complex!
After having spent hours with some of the RPCS3 team, we were able to come up with a method to not only make the emulator launch, but to launch into the game directly!
Read carefully because this is some complicated stuff.
First, make sure your launcher config is as such:
executable = emulators\PS3\rpcs3.exe
arguments = "%ITEM_FILEPATH%"
Next, you must place your ps3 game dump wherever it is you're going to be storing them. For me, I stored them in the roms folder themselves for portability reasons.
Next, and this is the absolute most important part. Go to the settings file in the ps3 folder in collections and change the file type to BIN, not bin. It must be capitalized.
Next, you need to launch your command prompt as an administrator and type
mklink "1" "2"
replace 1 with the path to the folder where you wish to place the shortcut. This is like an advanced shortcut, because it has to be. You cannot right click the EBOOT.BIN file and create a shortcut that way. RetroFE won't read the directories correctly that way. Doing it this way creates what's called a SymLink. It's an advanced type of shortcut that uses the same file extension as the file it's being directed to, allowing you to open that file using pathing, like in this case. Replace 2 with the path to the bin file you're creating a shortcut for.
So for me I typed in this:
mklink "R:\collections\Sony Playstation 3\roms\Ratchet and Clank Trilogy.BIN" "R:\collections\Sony Playstation 3\roms\Ratchet and Clank Trilogy\PS3_GAME\USRDIR\EBOOT.BIN"
Remember, the first set of quotations is the name and location of the shortcut you want to make, and the second set of quotations is the path to the binary file you're making the shortcut of.
Following all of these directions carefully will allow you to launch the game from RetroFE directly through RPCS3 and into the game!
