PKG successfully installs but game doesn't show up on game list?

Also EBOOT.bin is not on the Game folder, but in the Game folder's subdirectory PS3_GAME -> USRDIR.
In your case it is in Desktop/rpcs3-v0.0.4-2018-02-06-5b5f2d42_win64/dev_hdd0/game/NPEB01158/PS3_GAME/USRDIR/EBOOT.bin

If you can't find it there then I suppose it is what Ani said. If you can't manage to unpack it you can always download it.. as long as you have it also original I think that's okay and could be considered a backup(?)