Basically the problem is that for Armourer's Workshop armors that disable the normal renderer, they don't disable it when skin port is installed (probably due to SkinPort using a different renderer i suppose) resulting in the armor conflicting with the player model.

I know this mod is old and i'm not expecting you to take your time to make a update or even take your time to fix it but having guidance to fix it myself could be cool, do you have any clues where is the bug coming from and a possible workaround?

If I remembered correctly, armors don't disable player model rendering, they just overlay a slightly larger box on top of the player model.
And by the look of your screenshot, because of the newer clothing layers, it is causing z-fighting with armor layers.
Either making the armor model slightly larger or making the player model slightly smaller should work.
You can also just disable the extra clothing layers through skin customization in the options menu, when wearing those armors.

It seems like even without extra layers it still cause skin glitches

Well, you can modify SkinPortRenderPlayer in SkinPort to make it skip rendering when armors from AW is equipped.