If you can do one, why not do the other?
If the area of the card that stored the actual rom was rewritable, we would have hacked games long ago, back when we found you could dump roms with a flashcart. The only non-ROM data on the card is the save.
But you don't need to write to the ROM to hack it. Aside from replacement hacks (replacing sprites, adding in new features or areas, etc) most everything else can be achieved with memory patching (read: Action Replay; NitroHAX). Those can be used for temporary hacks (or things that will be written to the save file upon save). Otherwise, you can mod the save (give yourself items, weapons, more health, etc) but that is fairly limited. Most of the time you can't mod a save to give yourself infinite armor, because the save will only hold how much armor you have. You could give yourself uber amounts (if the game supports it) but if you want infinite armor you would have to patch variables in memory to have, for lack of a simpler explanation, the variable(s) that hold how much armor you have turn into a constant value. But if you give yourself an item with an ActionReplay, that will usually persist through a save, or you could mod it right into the save.
We're not looking to write a new ROM, we're curious if we will at some point be able to read the ROM with this.