A sample spine-unity shader substitute for the Spine/Skeleton shader that allows filling pixels with a certain color _FillColor, with a custom alpha _FillAlpha.

SampleSkeletonFillUse.cs

using UnityEngine;
using System.Collections;
using Spine;
using Spine.Unity;

public class SampleSkeletonFillUse : MonoBehaviour {

	MeshRenderer meshRenderer;
	MaterialPropertyBlock block;

	IEnumerator Start () { // Start as a coroutine.
		var state = GetComponent<SkeletonAnimation>().state;
		meshRenderer = GetComponent<MeshRenderer>();

		block = new MaterialPropertyBlock();
		meshRenderer.SetPropertyBlock(block);

		while (true) {
			yield return new WaitForSeconds(1f); // Wait 1 second.
			state.SetAnimation(0, "hit", false); // Play hit animation.
			state.AddAnimation(0, "idle", true, 0f); // Queue idle animation.
			StartCoroutine(FlashRoutine()); // Flash the fill color.
		}
	}

	IEnumerator FlashRoutine () {
		const int Flashes = 4;

		// You can use these instead of strings.
		int fillAlpha = Shader.PropertyToID("_FillAlpha");
		int fillColor = Shader.PropertyToID("_FillColor");

		for (int i = 0; i < Flashes; i++) {
			block.SetFloat(fillAlpha, 1f); // Make the fill opaque.

			block.SetColor(fillColor, Color.white); // Fill with white.
			meshRenderer.SetPropertyBlock(block);
			yield return null;

			block.SetColor(fillColor, new Color(0.8f, 0, 0)); // Fill with red.
			meshRenderer.SetPropertyBlock(block);
			yield return null;

			block.SetFloat(fillAlpha, 0f); // Remove the fill.
			meshRenderer.SetPropertyBlock(block);
			yield return null;
		}			
	}

}

SkeletonFill.shader

//Skeleton Fill
// - Unlit + no shadow
// - Premultiplied Alpha Blending (One OneMinusSrcAlpha)
// - Double-sided, no depth

Shader "Spine/Skeleton Fill" {
    Properties {
        _FillColor ("Fill Color", Color) = (1,1,1,1)
        _FillAlpha ("Fill Alpha", Range(0, 1)) = 0
        [NoScaleOffset]_MainTex ("Main Texture", 2D) = "white" {}
    }
    SubShader {
        Tags { "IgnoreProjector"="True" "Queue"="Transparent" "RenderType"="Transparent" "PreviewType"="Plane" }
        LOD 100

        Blend One OneMinusSrcAlpha
        Cull Off
        ZWrite Off
        Lighting Off

        Pass {
            CGPROGRAM
            #pragma vertex vert
            #pragma fragment frag
            #include "UnityCG.cginc"
            uniform sampler2D _MainTex;
            uniform float4 _FillColor;
            uniform float _FillAlpha;

            struct VertexInput {
                float4 vertex : POSITION;
                float2 texcoord0 : TEXCOORD0;
                float4 vertexColor : COLOR;
            };

            struct VertexOutput {
                float4 pos : SV_POSITION;
                float2 uv0 : TEXCOORD0;
                float4 vertexColor : COLOR;
            };

            VertexOutput vert (VertexInput v) {
                VertexOutput o = (VertexOutput)0;
                o.uv0 = v.texcoord0;
                o.vertexColor = v.vertexColor;
                o.pos = mul(UNITY_MATRIX_MVP, v.vertex);
                return o;
            }

            float4 frag (VertexOutput i) : COLOR {
                float4 rawColor = tex2D(_MainTex,i.uv0);
                float finalAlpha = (rawColor.a * i.vertexColor.a);

                float3 finalColor = lerp((rawColor.rgb * i.vertexColor.rgb), (_FillColor.rgb * finalAlpha), _FillAlpha);
	            return fixed4(finalColor, finalAlpha);
            }
            ENDCG
        }
    }
    FallBack "Diffuse"
}