Re: uniquely fingerprint aeroplanes
You could have multiple transponders on an aircraft, but if the fingerprinting can identify one it can identify all.
So potentially you would need to manufacture a new transponder to fit to each airframe every time you wanted to avoid tracking by this method.
Certainly not beyond the means of the military if they want to spaff the cash.
You could go ADS-B (maybe Mode A/C too) silent, but primary radar will pick you up so spoofing secondary radar might have some value in giving you a free pass.