...they could but are they doing it ? Do you know whom to ask ? Do you know whether you even have the right to ask these questions and get an answer ? ...and if you get the answer that they are not doing it and instead a private entity will handle it, will you have a choice to not link your PAN card to Aadhaar ?
If I can't believe that they are following the law, my data is already public. I remember there was a debate sometime back where income tax info was needed to decide whether you qualify for certain subsidies or not and there was no way to get the income tax data even for the govt (different dept).
Income tax aadhar linkage should not be optional in the same way paying taxes isn't (in my opinion). I mean only 10-2000000 above with more than 1000000 rs income (declared). That's just disgusting.