as far as EASA land is concerned a pilot may be flying legally even though by any other international standard he may be illegal
No. It is simple. EASA are adding and not substituting. If you fly a 3rd country aircraft in Europe complaint with EASA but not the state of registry you are still illegal.
This as a matter of principle seems wrong and violates what courts in international terms refer to as the comity of nations.
It doesn't. There is vast precedent in ICAO and international law that countries have sovereignity over their airspace, and can impose regulations on their citizens, including not permitting them to operate 3rd country aircraft within their home state. I am sorry. There are plenty of, what seem to me, valid arguments, against what EASA are doing and "violating the comity of nations" isn't one of them. Isn't violating the rights of citizens not to have bad, politically-motivated regulation imposed on them enough?
I don't think you can make such a sweeping statement without some evidence to back it up. The sort of people who will be caught by these rules are just the sort of people likely to have ambiguity over their residence or where they are established. So, if a pilot is asked to sign a declaration and refuses, the sanction is what? He has an address in New York and one in London! So far this year 60% of his time has been spent in London but his intent is to spend the rest of the year in New York. Where is he resident for these purposes?
The reason I said 99% is that I think it reasonably captures the fact that a great majority of people impacted are unambiguously resident in the EU. Where is your evidence for the sweeping claim that "the sort of people who will be caught by these rules are just the sort of people likely to have ambiguity over their residence"? Hey, if people aren't resident in the EU and can establish reasonable grounds for this, I suspect they have nothing to worry about. It's the rest who are worried.