Solution
When using the RFmx Python API and calling the load_s_parameter_external_attenuation_table_from_s2p_file function to load and store the S-Parameter table from the S2P file for de-embedding, you must first commit the scalar de-embedding factors to the instrument before attempting to set your reference level to a higher value than what is normally allowed.
During your instrument session configuration, you will first call the load_s_parameter_external_attenuation_table_from_s2p_file and then call the RFmx SpecAn Commit function (or which ever RFmx personality is being used). Once you have committed the scalar de-embedding factors to the hardware, then you can call the configure_reference_level function to set your desired reference level.
As an example, the following code snippet is a minor edit of the example from the RFmx SpecAn Python API Documentation. This snippet shows loading the external attenuation table from an S2P file, committing the instrument settings, then configuring the reference level before initiating the measurement.