Alpha Texture Deserves a Separate File?

I've searched through numerous forum threads and still no clear one answer if it requires a separate file.

When I'm modeling a character with hair that requires a transparent bumped diffuse for example, I see the whole model becomes flashy and can see through at some area of the model.

My question is, do I need to create another texture file solely dedicated to any alpha texture away from the normal bumped diffuse texture? If I were to combine everything into one file, what's the best solution to avoid that problem?

Any tips, links to already discussed thread, direct answers are much appreciated. Thanks in advance for reading.