how to programmatically allow Unity Shader to control which object renders in front?

In the gif below both objects are colliding and according to the camera position the cube is in front of the sphere but I can change their visibility with the render queue:

If that's what you want you only have to add ZWrite Off in your subshader before the CGPROGRAM starts, the following is the Standard Surface Shader including the line:

Shader "Custom/Shader" {
Properties {
    _Color ("Color", Color) = (1,1,1,1)
    _MainTex ("Albedo (RGB)", 2D) = "white" {}
    _Glossiness ("Smoothness", Range(0,1)) = 0.5
    _Metallic ("Metallic", Range(0,1)) = 0.0
}
SubShader {
    Tags { "RenderType"="Opaque" }
    LOD 200
    ZWrite Off 
    CGPROGRAM
    // Physically based Standard lighting model, and enable shadows on all light types
    #pragma surface surf Standard fullforwardshadows

    // Use shader model 3.0 target, to get nicer looking lighting
    #pragma target 3.0

    sampler2D _MainTex;

    struct Input {
        float2 uv_MainTex;
    };

    half _Glossiness;
    half _Metallic;
    fixed4 _Color;

    // Add instancing support for this shader. You need to check 'Enable Instancing' on materials that use the shader.
    // See https://docs.unity3d.com/Manual/GPUInstancing.html for more information about instancing.
    // #pragma instancing_options assumeuniformscaling
    UNITY_INSTANCING_BUFFER_START(Props)
        // put more per-instance properties here
    UNITY_INSTANCING_BUFFER_END(Props)

    void surf (Input IN, inout SurfaceOutputStandard o) {
        // Albedo comes from a texture tinted by color
        fixed4 c = tex2D (_MainTex, IN.uv_MainTex) * _Color;
        o.Albedo = c.rgb;
        // Metallic and smoothness come from slider variables
        o.Metallic = _Metallic;
        o.Smoothness = _Glossiness;
        o.Alpha = c.a;
    }
    ENDCG
}
FallBack "Diffuse"
}

Now sorting particles, look at the shadows and how they collide and how we can change their visibility regardless of their position.

Here's the shader for particles, I'm using the Unity Built-in shader, the only thing added is Ztest Always

     Shader "Particles/Alpha Blended Premultiply Custom" {
 Properties {
     _MainTex ("Particle Texture", 2D) = "white" {}
     _InvFade ("Soft Particles Factor", Range(0.01,3.0)) = 1.0
 }

 Category {
     Tags { "Queue"="Transparent" "IgnoreProjector"="True" "RenderType"="Transparent" "PreviewType"="Plane" }
     ZTest Always
     Blend SrcAlpha OneMinusSrcAlpha
     ColorMask RGB
     Cull Off Lighting Off ZWrite Off

     SubShader {
         Pass {

             CGPROGRAM
             #pragma vertex vert
             #pragma fragment frag
             #pragma target 2.0
             #pragma multi_compile_particles
             #pragma multi_compile_fog

             #include "UnityCG.cginc"

             sampler2D _MainTex;
             fixed4 _TintColor;

             struct appdata_t {
                 float4 vertex : POSITION;
                 fixed4 color : COLOR;
                 float2 texcoord : TEXCOORD0;
                 UNITY_VERTEX_INPUT_INSTANCE_ID
             };

             struct v2f {
                 float4 vertex : SV_POSITION;
                 fixed4 color : COLOR;
                 float2 texcoord : TEXCOORD0;
                 #ifdef SOFTPARTICLES_ON
                 float4 projPos : TEXCOORD1;
                 #endif
                 UNITY_VERTEX_OUTPUT_STEREO
             };

             float4 _MainTex_ST;

             v2f vert (appdata_t v)
             {
                 v2f o;
                 UNITY_SETUP_INSTANCE_ID(v);
                 UNITY_INITIALIZE_VERTEX_OUTPUT_STEREO(o);
                 o.vertex = UnityObjectToClipPos(v.vertex);
                 #ifdef SOFTPARTICLES_ON
                 o.projPos = ComputeScreenPos (o.vertex);
                 COMPUTE_EYEDEPTH(o.projPos.z);
                 #endif
                 o.color = v.color;
                 o.texcoord = TRANSFORM_TEX(v.texcoord,_MainTex);
                 return o;
             }

             UNITY_DECLARE_DEPTH_TEXTURE(_CameraDepthTexture);
             float _InvFade;

             fixed4 frag (v2f i) : SV_Target
             {
                 #ifdef SOFTPARTICLES_ON
                 float sceneZ = LinearEyeDepth (SAMPLE_DEPTH_TEXTURE_PROJ(_CameraDepthTexture, UNITY_PROJ_COORD(i.projPos)));
                 float partZ = i.projPos.z;
                 float fade = saturate (_InvFade * (sceneZ-partZ));
                 i.color.a *= fade;
                 #endif

                 return i.color * tex2D(_MainTex, i.texcoord) * i.color.a;
             }
             ENDCG
         }
     }
 }
 }