Ah, I see. I thought it would have automatically generated default settings for each Warp3D application you could edit from a preferences editor. It is clear now.
The reason I chose to do it this way was the fact that the drivers already used environment variables to change their global options. Rather than introduce a completely new (from the user's perspective) way of managing settings, it seemed more natural to extend the existing one.
The fact that the application settings will always override the global ones (which in turn will always override the compiled-in defaults) gives you some flexibility in how you manage things. Aside from the obvious use case of enabling something just for one application that is disabled by default, you might decide that the compiled in default for a particular feature is not what you want, except for one application. In that case, you could disable it in the global settings and then re-enable it in the settings just for that app.
In my case, for example, almost none of my Warp3D-using software uses a stencil buffer. I could therefore turn on "Use16BitZBuffer" globally for my Radeon 7000 and disable it again for the minority. The default 24-bit depth buffer with 8 unused bits of stencil is a waste of VRAM and bandwidth for the rest.