It's because the effect is hotwired to use additive blending, which means that if the diffuse texture is RGB map, black is interpreted as transparent, and this is basically the same thing as glow mapping to begin with. That's why it probably doesn't even look for -glow textures; it has no need for them in normal use.
You'll have to save the diffuse texture with white alpha channel to make it opaque. Even then it won't be true diffuse texture, since lighting is not applied to effects like 3D shockwave or 3d warp.
Of course, you can play around with some serious hackery trickery.
Use a 16x16 black texture for warp effects.
Make a ship entry that uses warp.pof as a model. Make sure it doesn't have working collision detection (ie. you can fly through the model).
Make a mission SEXP series or script that creates the "ship" warp model in front of a ship that is warping out. That would technically allow you to do whatever you want with the warp.pof model (or whichever model you want to use) but I predict some serious if not impossible timing / synching issues with the effect popping into existence, getting the animation timed so that the ship in question will have time to disappear through the invisible portal, and whatnot.
But it's most likely possible. Horrible hack, but possible.
I wouldn't bother.
