Download play is different from wifi and to the OP, I'm sure it would work if you used the same .sav. The reason Nintendo tells you that the FC will be tied to the NDS and game itself is because the "game" (original cartridge) is holding the save information, which makes that cartridge unique from Joe's cartridge across the street. Since you can replace the save with flash carts, the only thing tied to it would be the NDS itself (that information is still held in the save as well ;p). To summarize, both things that are tied to the FC are held in the save so you could take the rom off and put it back on later and as long as you're using the same save, it doesn't know you did a thing.