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There is nothing exploitative when evaluating these two options:

* Patching the binary locally without its source code to do what I want it to do

* Submitting a patch upstream to an open source project

and arriving at the conclusion that the latter is preferable.

Yes there is, because the for-profit organisation making you sign a CLA for your contributions is effectively using your free labor to suppress wages of its employees.

Doing free work for an employer is always parasitic with regards to its employees.

You have a third option here which you didn't list, which is forking the project into one which is working in favor of the public; removing the CLA and giving each contributor shared ownership of the project. Your contribution should then be made to that project.

I can't fork the project into something that ships with the OS.

That's fine, people can still load your program onto it themselves.

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