The only difference is that "from start" movies don't contain SRAM, which could theoretically allow cheating, or at least skipping introductory parts of the game which would make runs hard to compare. All existing SNES submissions are from reset with SRAM and we just have to trust that they don't actually use it. I thought it would be better for it to be an option to have none at all so it's not even a possibility that a run could rely on previously saved data. There is further explanation at the
rules page under "The movie must begin from console power-on".
It shouldn't be necessary for you to start over. If you're really not relying on the save data, it should work to hex edit it away. (Actually, it should be as simple as changing byte 0x014 to 0.) Anyway, I think in this case it's not a huge deal since you start a new game in the movie and there don't seem to be any other existing save slots so the SRAM saved in the movie is most likely empty and unused by the game. But avoid starting any new movies from reset if they're intended for submission.