The perception that the Mindy is more versatile is rather false; both the Daisy and Mindy are capable of mounting the same accessories.
As far as I know, the Mindy is for space use, which does include boarding, and general support of starships and starfighters, even if it's not as powerful, the Mindy is considerably more Maneuverable than any starfighter, and being smaller, makes a much more difficult target to hit. The Mindy is also generally used for aerial support, as well as for very quick blitz-like missions due to its speed and capability for use of a variety of weapons. The Mindy's key attributes are its speed and Mobility, and its generally used in short-range missions that don't last very long.
The Daisy is capable of mounting all the same weapons and accessories. The Daisy is indeed, more heavily armored, and is meant for more ground-based use. While capable of flight and even usable in space, it is not designed for those uses and not very good at them; the flight capability is more of an extended jump, to reach higher positions or get a temporary better vantage point, or to increase the speed of movement between two points. However, it lacks the same kind of speed and agility, instead being more stable to counteract the forces encountered during planetary combat.
In short, the Mindy is for high speed blitz combat, while the Daisy is better for more drawn-out, ground based engagements.