where IN is the output from the frequency phase detector, OUT is the low pass filter output.
What is the difference between (A) and (B)? Any comments/hints?
The main difference is the parasitic capacitance from each node to ground and their affect on the performance. If this is inside an IC these capacitances can be very large. In discrete designs they are small.
It is inside the IC. From the perspective of transfer function, both configurations are the same. What is the effect of the different configuration on performance?
Which is preferred in practical circuit?