1. Since the story's mainly focused on these 3, and since it's an RPG, technically yes, they're playable, though I'm actually coming up with a fourth character to join the party later on...
2. The differences between the characters are basically their stats. Miki, being the lead, has her stats balanced. Sure, she has the most usage of magic, but she's decent enough for attacks as well. Bosko, while knowing a bit of magic himself, is a bit more on the defensive side, since he's her main partner throughout the game. Phineas, on the other hand, is more on offense, since he doesn't know any magic, but can use a variety of weapons, including a laser gun he built from the beginning (as I said before, he's the equivalent to Jeff from EarthBound).
3. Since the game is an RPG, health will probably be displayed through numbers and such. And yes, similar to a lot of RPGs, there's a lot of ways to heal, either through Miki's magic, or healing items such as food or drinks. As for characters falling, basically, if one character falls because they're out of health, there are ways to revive them, either through magic, or the overworld. However, if ALL party members fall because they get damaged too much, it's an instant game over.