What? Powersaves only collects data from your cartridge before sending it to their servers.
All alterations are done outside of their program, on their servers.
Communications work like this:
CartReader gets ROM data -> Transmit to Datel
Datel transmits back the encrypted card-reading commands (this is why online is required).
The CartReader gets the save data -> Codes / Options are now shown.
If you choose codes, you send off your ROM data and Save file, and then they apply the codes, send you back the edited save file, then the dongle writes the save using the stored card-reading commands.
It's not a simple process; the 3DS has some very intense encryption which cannot be emulated by a computer program. Your ideas are not new; if it was possible it would already be done.