I don't see how 8K chunks are so bad. Think of it like a disk with 8K clusters. You store the level that the user is building in $7F0000-$7FFFFF, then you save it out to $006000-$007FFF, $016000-$017FFF, ..., $3F6000-$3F7FFF.
But in practice, I'm not sure how the user is going to be able to fill 512K with just a controller. Are you planning to support a Super NES Mouse? Could you give a short breakdown of how the 512K will be allocated? Because
Dezaemon uses only 128K. Even
Animal Crossing: Wild World for DS only uses 88K or so out of the 256K serial flash in the Game Card, with the rest used for a backup copy in case saving goes wrong and for letters stored at the Post Office, and much of that is used with developer time prioritized over space. And a few years ago, we
discussed how to
simplify the design to cut the save file to under 32K.