Here I have the UV mab for an .obj file:
In three.js:

As you can see, this out-of-bounds faces are colored as black. How can I instead have them become transparent? (It is not an option to put them in-bounds with a transparent area of the texture)
Here I have the UV mab for an .obj file:
As you can see, this out-of-bounds faces are colored as black. How can I instead have them become transparent? (It is not an option to put them in-bounds with a transparent area of the texture)
UV maps have no in-bounds or out-of-bounds areas. Every pixel of them could be (and will be) used as a texture when some UV coordinates point to them.
If you do not want to use alpha maps (as this is the default way to have texture-base transparency), you might consider customizing the fragment shader to discard fragments (pixels) that fall in the out-of-bounds area. For this, you also have to implement a way for the shader to distinguish what is in and what it out either by filtering the UV coordinates, or by filtering the color from the texture.
I might have misunderstood your question. If this is the case, I’m sorry.