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The GNSSSignalMag.vi is missing. Is it part of some toolkit?
I replaced the Express Simulation VI with Sine Waveform.vi from the Signal Conditioning palette so that I can control things like Fs. When I do that and look at the maximum value in the adjusted spectrum, it remains the same whether windowed or not.
Extract Single Tone Information.vi uses FFT techniques for measuring tone information. You can open its block diagram to see how NI did things.
It has been a while since I used MATLAB but I think they use a different scaling method for FFT.