Many people attack companies that use tax loopholes even though the government does "allow" these loopholes. So if one is opposed to something, but it is formally allowed, one should attack both sides: The people doing it and the government.
Your correlation doesn't hold up because tax loopholes are not formally allowed. You call that out in your previous sentence by scare-quoting "allow". The inventor uses a formal system (patents). The company uses an informal system (tax loopholes). In the case of a formal system, you do not attack the inventor because he is just using the proper channel. In the case of an informal system, you do attack the company because the company is unethically taking advantage of a channel that shouldn't be there in the first place.
[0]: The original "Free as in speech" seems to be a much better way to express your sentiment.
https://en.wikipedia.org/wiki/Alice_Corp._v._CLS_Bank_Intern...
The boundaries are fluent (FPGAs).
