これを適当なGameObjectに貼り付けることで、Shift+Sで通常撮影(透明度ナシ)、Shift+Gで透明度あり撮影を行うことができます。

ScreenShot.cs

using System;
using System.Collections;
using System.IO;
using UnityEngine;

namespace Negipoyoc.SS
{
    public class ScreenShot : MonoBehaviour
    {
        void Update()
        {
            if (Input.GetKeyDown(KeyCode.S) && Input.GetKey(KeyCode.LeftShift))
            {
                ScreenCapture.CaptureScreenshot(DateTime.Now.ToString("yyyy-MM-dd_HH-mm-ss") + ".png");
            }
            if (Input.GetKeyDown(KeyCode.G) && Input.GetKey(KeyCode.LeftShift))
            {
                StartCoroutine(CaptureWithAlpha());
            }
        }

        IEnumerator CaptureWithAlpha()
        {
            yield return new WaitForEndOfFrame();

            var tex = ScreenCapture.CaptureScreenshotAsTexture();

            var width = tex.width;
            var height = tex.height;
            var texAlpha = new Texture2D(width, height, TextureFormat.ARGB32, false);
            // Read screen contents into the texture
            texAlpha.ReadPixels(new Rect(0, 0, width, height), 0, 0);
            texAlpha.Apply();

            // Encode texture into PNG
            var bytes = texAlpha.EncodeToPNG();
            Destroy(tex);
            File.WriteAllBytes(Application.streamingAssetsPath + "/" + DateTime.Now.ToString("yyyy-MM-dd_HH-mm-ss") + ".png", bytes);
        }
    }
}