I have taken to rolling the final R in niner (and elesewhere), the way I think it is done colloquially in Scotland. After all it was added by ICAO for the sake of unambiguity so I can best make it stand out. Never got any comments.
As for "tree" versus "three", I have never used a radio that allowed hearing the difference.
Agreed with with Genghis that it is NOT done to correct people on their pronounciation, except where absoltutely necessary for the clarity of communications. Wasn't it a basic principle to keep the frequency as unoccupied as possible?
And while we're on the subject of non-native speakers: French and Italians are quite easily picked out by their accent, no need for cues - and if you hear someone pronouncing "zero" as "see-row" you can bet he's Dutch.