Hi Ankit,
You are correct that the FRF (Mag & Phase) VIs are very similar. The one provided with the Sound and Vibration Toolset has several extra features such as the Spectrum Info output.
For a given measurement with given settings you could choose either VI, however you should see the same result from both. If you are not seeing the same result, I expect the input parameters are not identical. Changining input parameters such as averaging can have significant impact on your results. Verify that you have identical parameters and I expect you will be able to get your results to match.
Regards,
Jennifer O.
Applications Engineer
National Instruments