shader not working as intended after transitioning from OpenGL ES 2 to OpenGL ES 3 on Android device

So I have a Unity plugin for an Android app split into two parts written in c++ (generating two separate .so files ).
For discussion purposes I'm going to redact and simplify what they do:

first what my c# script does:

Code (CSharp):

1. colorTexture = new Texture2D(width, height, TextureFormat.ARGB32, false);
2. externalPluginA.sendID(colorTexture.GetNativeTextureID());
3. alphaTexture = new Texture2D(width, height, TextureFormat.Alpha8, false);
4. externalPluginB.sendID(alphaTexture.GetNativeTextureID());
5.  

now for what externalPluginA does with the first pointer:

Code (C++):

1. glBindTexture(GL_TEXTURE_2D, textureID);
2. glTexSubImage2D(GL_TEXTURE_2D, 0, 0, 0, width, height, glPixFormat, glPixType, frameBuffer->buff);

(frameBuffer->buffer is the raw output of the camera, but we can just assume it's a colored image. I can't check what glPixFormat and glPixFormat are at runtime but that should be irrelevant as you will soon see.)

and what externalPluginB does with the second pointer:

Code (C++):

1. static std::vector<unsigned char> emptyPixelsAlpha(height * width, 0);
2.  
3. glBindTexture(GL_TEXTURE_2D, alphaID);
4. glTexSubImage2D(GL_TEXTURE_2D, 0, 0, 0, width, height, GL_ALPHA, GL_UNSIGNED_BYTE, emptyPixelsAlpha.data());

this just fills the alpha channel of this texture with zeros, interpretable as a fully transparent alpha channel.

colorTexture and alphaTexture are then fed to a material that has this shader:

Code (shader):

1.  Shader "alphaMaskShader"
2. {
3.     Properties{
4.       _MainTex("Base (RGB)", 2D) = "white" {}
5.       _Alpha("Alpha (A)", 2D) = "white" {}
6.     }
7.     SubShader{
8.         Tags{ "RenderType" = "Transparent" "Queue" = "Overlay" }
9.  
10.         ZWrite Off
11.         ZTest Off
12.  
13.         Blend SrcAlpha OneMinusSrcAlpha
14.         ColorMask RGB
15.  
16.         Pass{
17.             SetTexture[_MainTex]{
18.             Combine texture
19.             }
20.             SetTexture[_Alpha]{
21.             Combine previous, texture
22.             }
23.         }
24.     }
25. }

what this does is simply use alphatexture as the alpha channel for colorTexture, and given that we filled alphaTexture with black it will give as output a fully transparent texture.

The fact is this worked perfectly well up until I decided to switch from OpenGL ES 2 to OpenGL ES 3.
To transition from one to the other I set OpenGL ES 3 as my Graphics API on Unity and in my two plugins I included GLES/gl3.h headers instead of GLES/gl2.h. The device I'm building on is a OnePlus 3 which supports OpenGL ES 3.

what it does now is show the colorTexture fully opaque, as if the alphaTexture were set to opaque. I don't see any particular errors in the log any it isn't crashing or anything.
The funny thing is that I decided to open up GAPID and record a trace, and lo and behold the frames shown in GAPID when analyzing the trace are displaying correct functioning, with the texture being completely transparent. I have no clue how this is possible and therefore ask for your help in figuring this out.