Feel free to open a thread about morality!
But you have to be aware that one person's morals are not the other person's morals and that this generally has to be accepted in a free society. Therefore laws exist to put real limits on what one is allowed to do.
In my view copyright doesn't have too much to do with "fair competition" between chess engines. Copyright allows you to reimplement each and every idea in Stockfish and all its evaluation parameters to get a functionally equivalent engine that is free of SF's copyright. (You will have to be careful about renaming variables etc. Basically you must make use of the liberty you have to express things differently while maintaining functionality including speed.) But such a functionally equivalent engine should obviously be regarded as a pure clone if it is about competition between chess engines.
Copyright law was simply not designed to ensure that "legal" engines are not "clones". (Nor was copyright law designed to perfectly suit the purposes of the FSF. The FSF makes clever use of copyright law with its GPL, but copyright still puts a limit on the GPL's effectiveness.)
So ultimately it is simply up to the tournament organiser to decide which engines to include and to the tester which engines to test (unless copyright law prevents him or her from including or testing a particular engine).
As far as "fairness" between programmers is concerned, it is a fact that different engines have widely different resources put into it. We are long past the point where one could reasonably consider competition between engines to be a "fair" contest among programmers.
If I am not mistaken, in the Shogi world programmers are allowed to start from a common base of source code and can then add their "secret" improvements (to be shared afterwards, perhaps). Not a bad idea if the goal is to measure programming ability.
