Look at it this way: id had these games laying on a shelve somewhere, unable to sell them because they didn't work on modern OS'es. Along comes this free, open software called DOSBox, and suddenly those long dead programs gets a new shelve life. Who should benefit from this? id+Valve only? DOSBox only? Or both parties?
Valve could have approached the DOSBox folk and negotiated a license that allowed them to link DOSBox with their checking code. I have no idea what such a deal would have costs them, or if it could have been made at all.
Instead the GPL at least tries to guarantee that the DOSBox people get something for their work: Access to part of Valve's source code.
And - GPL doesn't really make it difficult to protect your IP. You are entirely free to use it GPL'ed tools in your development process. You are even free to use the GPL'ed code for internal test and production use. You can treat and process customer data with it - as long as you/your company is doing the processing. But you CAN NOT license your product and its share of GPL'ed code to a 3rd party under a non-GPL license.
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