It's been the subject of debate. For a long time, and even on Sega Retro, there was a rumor that it was literally the SMS cart on a Sega Mega Drive PCB, with the lines physically switched so it'd boot into SMS mode, but a person on SMS Power with the cart debunked this. Turns out the cart lines are not physically jumped, so it doesn't boot directly into SMS mode, and when he dumped the cart, it was actually a different build from all known SMS builds (but actually matches the build on the Sega Saturn rerelease of phantasy star). It uses software mapping to force the Mega Drive into SMS mode, not hardware mapping. How it does this isn't understood well. Part of the mystery is that the JPN version of Phantasy Star uses the SMS Bios to set up the stack pointer, which the Mega Drive lacks. So it apparently has some bootstrapping code that is run before the game starts.