Tuning to a drone is more accurate than using a visual tuner. If you want to develop the muscle memory to be in tune quickly when you play the flute, looking at the "green light" or the 0% mark on a visual tuner can hold you back.
This is because a visual tuner sets the green light or 0% at the same location in Hz as the piano - which is equally spaced out in Hertz to closely approximate the notes found in the harmonic series. What sounds and feels most in tune to us may be a little bit off from center. The note a major 5th away from the drone, for example, will look a tad sharp on the visual tuner and the Major 3rd will look a tad flat. Our ears & bodies can naturally feel the most "in tune" harmonics, though it can take practice to learn to identify and name the most common intervals. And with practice & training we can learn to quickly match them on the flute. But if your perception of what's in tune is skewed by lots and lots of time with the visual tuner without using your ears, you may sound out of tune when playing with others. Don't be that guy or gal with a tuner on your stand who stands strong on the green light and refuses to budge on your tuning to the rest of the band, even if it would result in an overall better sound.
Don't get me wrong: visual tuners are a powerful and useful tool. However, use them with the knowledge that one day you will need to tune with your ears.