I seem tobe having some issues with the order its drawning or something like that.
Im using vertex colors.
If I set the alpha of the bottom vertices to 1 again I still get that draw issue on the top of the pillars.
If I set the queue to opaque it renders correctly, however the alpha renders as white (which would be expected as no transparencies in opaque queue)
Shader "Custom/VertexColors2" {
    Properties {
        _Color ("Color", Color) = (0,0,0,0)
        _MainTex ("Albedo (RGB)", 2D) = "white" {}
        _GridTex ("Grid Texture", 2D) = "white" {}
        _Glossiness ("Smoothness", Range(0,1)) = 0.5
        _Metallic ("Metallic", Range(0,1)) = 0.0
    }
    SubShader {
        Tags {"Queue"="Transparent" "IgnoreProjector"="True" "RenderType"="Transparent"}
        CGPROGRAM
        #pragma surface surf Standard alpha
        #pragma target 3.5
        sampler2D _MainTex;
        sampler2D _GridTex;
        struct Input {
            float2 uv_MainTex;
            float4 color : COLOR;
            float3 worldPos;
        };
        half _Glossiness;
        half _Metallic;
        fixed4 _Color;
        void surf (Input IN, inout SurfaceOutputStandard o) {
            fixed4 c = tex2D(_MainTex, IN.uv_MainTex) * _Color;
            float2 gridUV = IN.worldPos.xz;
            gridUV.x *= 1 / (4 * 8.66025404);
            gridUV.y *= 1 / (2 * 15.0);
            fixed4 grid = tex2D(_GridTex, gridUV);
            o.Albedo = c.rgb * IN.color * grid;
            o.Metallic = _Metallic;
            o.Smoothness = _Glossiness;
            o.Alpha = IN.color.a;
        }
        ENDCG
    }
    FallBack "Standard"
}
				
                        
I ended up adding a pass before the cg starts and it seem to be doing what I want it to do, still needs a little more tweaking though.