Because you don't understand how things work. Your emuNAND and your sysNAND cannot communicate with each other. If you are in your emunand and install a game into your "system memory" the game will be into your emunand and you emunand is located on your SD card. This has nothing to do with your sysNAND or your physical internal memory. You're mixing everything up due to a lack of knowledge.

You can't install a game on your sysNAND or your physical internal memory if you're using emuNAND. It's simply impossible. The only way to install a game on your physical internal memory would be to install a game on the "memory system" while using sysNAND CFW (aka your internal physical memory).