Thank you for your additional description, now I have understood the issue.
Yes, as soon as you make the diffuse texture transparent (also only a small part of it), the "opaque" parts/areas of it will become slightly transparent in-game too.
I am not an experienced person, but I think there are at least 2 solutions for this:
Use a .md3 model, with 2 different model parts/textures
One will be the model part which shall be totally opaque (with its own texture)
The other will be the transparent one (with its own texture)
Use any .mdx model format you want +
You can for example use the original .mdl model and make your replacement texture for it partialy transparent.
Then add a shader which only draws the parts of the diffuse textures, with a certain value
of transparency or less/more.
Something like this:
// cull disable // add this if you want to look "INSIDE" the soldier (with his back skin drawn !!)
GE128 means that only parts of the texture with greater alpha values will be drawn.
There is also LT128 which draws only smaller alpha values.
Be aware, that a hard limit means, there is now 'fluent' alpha possible (for example from fully opaque to fully transparent). For this you must use alpha blending
Nice Q3A shader descriptions can be found here
for example. There are of course also others.
Best of luck,
PS: I made some quick screenshots with the above mentioned and this test skin:
(I simply made a hole into the soldiers chest)
(complete texture becomes slightly transparent):
+ cull disabled
keyword (you can see the "inside" (= backside) of the model through the hole)
Be also aware, that as soon as a texture is transparent, its model will not cast shadows anymore ! You have to use the dpshadow
keyword to cast shadows again: