Well i dunno, the guide never mentioned installing cia to sysnand. Only after you install a9lh to the system and then enable luma and inject healty and safety to the nand which is all done on emunand before tranfering emunand to sysnand did it allow sysnand to install cia.To my knowledge any CFW that lets you run sysNAND (Such as rxTools, PastaCFW, MiniPasta and Luma I think) should let you install CIA's to the sysNAND, most people recommend either of the Pasta's as they are entirely sysNAND based CFW as they only boot sysNAND with signature checks patched.
So if anyone knows for sure about the gba vc games require double cia install to emunand and sysnand would be nice, or the person asking could just try it and find out.