This update is only for the textures. It has been made thanks to Zappy from SFM forums (who showed me the required guide) and turk645 ( who made the guide) from facepunch.
The idea for this feature came from seejayDJ's suggestion.

http://i.imgur.com/zsjzSv5.jpg
What has been changed.
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The VTFs.
They are now grayscale. But don't worry, the Alien Walkers will spawn with their default greenish-blue colors, only that they are controlled by two values: $selfillumtint (for the glow) and $color (for the base color, which you can see in the second skin or if you turn off $selfillumtint or just set it to the RGB values of 0 0 0 for the first skin).
A mask VTF was created for the body of the walkers, since only the eye of the customized Walker had one of these.
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The glow, base color and sheen can be recolored.
Add Override Materials, go to the materials and add the attributes for them with the following attributes:
Glow = vector 3 named $selfillumtint
color = color (or vector 3 if you plan to animate it later) named $color
sheen = vector 3 named $phongtint

The values for vector 3 are RGB in that order.
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The glow and color can be animated. Possibly the sheen too.
Conditions:
- all these attributes must be vector 3.
- you will need to spawn a prop with 3 bones if you want to change all three (one bone for each attribute and you must specify what attributes they control). If you only want to change the glow, a normal static_prop model is good enough.
- you will need knowledge regarding animating in the Graph Editor, as the RGBs will correspond to the X Y Z axis position.

Some of the people involved in this project might make a script to easily control all three of these, but until then you will have to follow this guide (skip step 1, because you can just add the attributes in the element viewer for the material nowadays) https://www.facepunch.com/showthread.php?t=1207260
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Changes to the models' materials
The Posable_Alien_Walker has separate materials for the eye and body, so you can change their attributes individually. The Posable_Alien_Walker_Original only has material for its entire body and now has slightly sharper lines around its eye since the texture was causing trouble with the placement of glow / color masks.