Sweeney himself says Musk's jet is using PIA. Sweeney told Musk about the program in the first place, so he was completely aware of the situation.
https://www.businessinsider.com/elon-musk-appears-use-faa-to...
https://www.businessinsider.com/elon-musk-appears-use-faa-to...
PIA only provides the anonymised codes, it's up to the aircraft owner to use them by recoding their transponder and as is clear from the evidence Musk's aircraft are using their original public codes.