Before anyone gets the wrong idea, this is a badly asked question.
System Config Tool when used to install games is no different than wupinstaller really. The main difference here is that it is an official Developer Tool, but as far as signed content goes, it listens to IOS-MCP (I think that's the right one). It does not have extra permission to install broken titles or anything as far as I am aware on a retail console.
If the game is using the Ticket bug which allows you to use a Disc Ticket with NUS Content, yes, it should work on redNAND and sysNAND.
If the content is using a patched/generated Ticket installed through redNAND/WUP fw.img, no it will not work on sysNAND alone. It *should* work with the wupserver fw.img though.
Personally I have not an SD card big enough quite yet, so I've been working with system nand. Lol