It is possible to continue past FlutterYay into the rest of the undeveloped game, where ponies begin to drop out and Pokemon fill in. To do so, go to Cheats->Cheat List...->Add gameshark and add this code:
This will allow you to walk through solid barriers, including the rocks behind Flutteryay. You can continue the game as usual, however you will be able to go through walls (including Flutteryay's barrier) and progress on to the game. Just fair warning: the areas beyond are not ready for standard play, and will contain glitchy Ponymon/Pokemon, tilesets, and may risk a crash in certain locations. Tread with caution.
Another more advanced option is to use Elite map\Advance Map. With it you can edit the game (including ponies, maps, and the majority of game functions). Deleting one of those blocking boulders should allow you access to the game, but this tool is far more complex than using cheat codes, and even more dangerous to use if you don't know what you're doing. It is recommended that you back up your ROM before using this tool, and use extreme caution.