Youhave a point about prefer_gl, provided that the code paths in
the browser for using GL are the same in its Windows and Linux
versions. But the other preference for disabling the shader
validator just opens the door to abuse.
Setting the "prefer_gl" preference on a Windows machine under Firefox is logically identical to testing the application under Linux or MacOS (and thereby forcing it to use OpenGL). If these "popular applications" work differently under different OS's then we have a problem that's much bigger than whether we allow users to flip the flag or not. ...
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