High output impedance from voltage source to a LPF?
Typicall function generators have a low output impedance amplifier in series with a 50 ohm resistor to the output BNC connector.

If you set the output to 50 ohms it will produce double the set amplitude at the amplifier output in anticipation of an external 50 ohm cable and termination dividing that voltage equally. If you apply only a very light load you will see that doubled voltage at the terminals.

If you set high impedance, the generator assumes very light loading and produces the set amplitude at the internal amplifier output node.

Your loading approaches 100 ohms at high frequencies so it is neither high nor low in comparison to 50 ohms, so to measure your filter response you should measure both the input and the output amplitudes.