The implementation is not ideal but there are workarounds. The black only needs to be slighly above absolute black to be transparent. For example, 0,0,1 won’t be transparent or 0,1,0. You only need to increase slightly the bright of the texture in Photoshop to avoid being transparent to the point that it won’t be noticeable. Then you can apply the alpha channel as a fully black color 0,0,0 over the image. The result could be confusing visually as in Photoshop black areas near to the new alpha black zone will look the same but will work. The texture will be aliased but if it has enough resolution it won’t noticeable.
If you want to avoid this workaround use zbrush zapplink then you can use Photoshop directly with your alphas.