Low C is sensitive to any leaks and one of the more difficult notes to get a big sound. It's easier with a C foot. The extra tube length of the B foot increases acoustic resistance, which tames and slows the response somewhat. Conversely, the C foot usually gives a faster response and brighter tone. How much difference it makes varies from one flute to the next - almost nothing on some flutes, to quite noticeable on others. Which is better also depends on the flute and the head. With a really bright flute, the C foot is too much and the B foot helps tame it. If the flute is on the dead side, the C foot can liven it up.
Middle C# is always on the sharp side. No flute scale is perfect and this is a compromise made in virtually all flute scales. C# being a short tube note, is the easiest to bend in pitch.