Your post sounds like it implies that other flash cartridges don't have this "problem"? I suspect they do and always will. If the game data are in the ROM file (*.nds ) and the personalized data are in the *.SAV file, then anytime the game uses friend codes it will be associated with that specific DS hardware.
But that shouldn't really be a "problem" though... If you put your commercial cart into a different DS than the one used initially, you just generate a new friend code. All that means is that prior friend code exchanges you've made are now invalid and you just need to go through the friend code exchange process again using your new one.
The flash carts, R4 included, should act no differently than a commercial cart in this regard.
striderx