When you change g, the maximum height the object reaches changes, so the second equation has two variables that are changing. You'd need to plug in a new value for g and d, which makes that equation difficult to use. It will eventually match the result of the first equation, but requires more work.
If you are launching at the same initial velocity, then the first equation is the easier one to use. If g decreases by a factor of 3, then the flight time increases by a factor of 3.