That's not a counterexample. The engine is free software and open source. There just isn't any free and open source material to run it on.
The same situation happens with Doom and Freedoom, but the existence or not of Freedoom doesn't change whether the Doom engine itself is open source or free.
After all, people are free to run the Doom engine on Freedoom. People are also free to do the same for Descent, I assume. If the Descent license were to forbid running Descent on your own custom-made game assets, then it would not be open source nor free software.
The same situation happens with Doom and Freedoom, but the existence or not of Freedoom doesn't change whether the Doom engine itself is open source or free.
After all, people are free to run the Doom engine on Freedoom. People are also free to do the same for Descent, I assume. If the Descent license were to forbid running Descent on your own custom-made game assets, then it would not be open source nor free software.