I ran in the same issue a few months ago and just ran across this post.  I was able to get around it by making my own Combres filter (FixUrlsInCSSFilter) that will read a "Base Url" value from the web.config or a database setting and apply it to all combres image urls. 
Hope it helps someone out there...
combres.xml:
<combres xmlns='urn:combres'>
  <filters>
    <filter type="MySite.Filters.FixUrlsInCssFilter, MySite" />
  </filters>
FixUrlsInCssFilter - most of this was copied from the original reflected file
    public sealed class FixUrlsInCssFilter : ISingleContentFilter
{
    /// <inheritdoc cref="IContentFilter.CanApplyTo" />
    public bool CanApplyTo(ResourceType resourceType)
    {
        return resourceType == ResourceType.CSS;
    }
    /// <inheritdoc cref="ISingleContentFilter.TransformContent" />
    public string TransformContent(ResourceSet resourceSet, Resource resource, string content)
    {
        string baseUrl = AppSettings.GetImageBaseUrl();
        return Regex.Replace(content, @"url\((?<url>.*?)\)", match => FixUrl(resource, match, baseUrl),
            RegexOptions.IgnoreCase | RegexOptions.Singleline | RegexOptions.ExplicitCapture);
    }
    private static string FixUrl(Resource resource, Match match, string baseUrl)
    {
        try
        {
            const string template = "url(\"{0}\")";
            var url = match.Groups["url"].Value.Trim('\"', '\'');
            while (url.StartsWith("../", StringComparison.Ordinal))
            {
                url = url.Substring(3); // skip one '../'
            }
            if (!baseUrl.EndsWith("/"))
                baseUrl += "/";
            if (baseUrl.StartsWith("http"))
            {
                return string.Format(CultureInfo.InvariantCulture, template, baseUrl + url);
            }
            else
                return string.Format(CultureInfo.InvariantCulture, template, (baseUrl + url).ResolveUrl());
        }
        catch (Exception ex)
        {
            // Be lenient here, only log.  After all, this is just an image in the CSS file
            // and it should't be the reason to stop loading that CSS file.
            EventManager.RaiseExceptionEvent("Cannot fix url " + match.Value, ex);
            return match.Value;
        }
    }
}
#region Required to override FixUrlsInCssFilter for Combres
public static class CombresExtensionMethods
{
    /// <summary>
    ///   Returns the relative HTTP path from a partial path starting out with a ~ character or the original URL if it's an absolute or relative URL that doesn't start with ~.
    /// </summary>
    public static string ResolveUrl(this string originalUrl)
    {
        if (string.IsNullOrEmpty(originalUrl) || IsAbsoluteUrl(originalUrl) || !originalUrl.StartsWith("~", StringComparison.Ordinal))
            return originalUrl;
        /* 
         * Fix up path for ~ root app dir directory
         * VirtualPathUtility blows up if there is a 
         * query string, so we have to account for this.
         */
        var queryStringStartIndex = originalUrl.IndexOf('?');
        string result;
        if (queryStringStartIndex != -1)
        {
            var baseUrl = originalUrl.Substring(0, queryStringStartIndex);
            var queryString = originalUrl.Substring(queryStringStartIndex);
            result = string.Concat(VirtualPathUtility.ToAbsolute(baseUrl), queryString);
        }
        else
        {
            result = VirtualPathUtility.ToAbsolute(originalUrl);
        }
        return result.StartsWith("/", StringComparison.Ordinal) ? result : "/" + result;
    }
    private static bool IsAbsoluteUrl(string url)
    {
        int indexOfSlashes = url.IndexOf("://", StringComparison.Ordinal);
        int indexOfQuestionMarks = url.IndexOf("?", StringComparison.Ordinal);
        /*
         * This has :// but still NOT an absolute path:
         * ~/path/to/page.aspx?returnurl=http://www.my.page
         */
        return indexOfSlashes > -1 && (indexOfQuestionMarks < 0 || indexOfQuestionMarks > indexOfSlashes);
    }
}
#endregion
AppSettings class - to retrieve the value from the web.config.  I also use this to build the path for images not handled by combres...
    public class AppSettings
{
    /// <summary>
    /// Retrieves the value for "ImageBaseUrl" if the key exists
    /// </summary>
    /// <returns></returns>
    public static string GetImageBaseUrl()
    {
        string baseUrl = "";
        if (ConfigurationManager.AppSettings["ImageBaseUrl"] != null)
            baseUrl = ConfigurationManager.AppSettings["ImageBaseUrl"];
        return baseUrl;
    }
}
web.config values
<appSettings>
   <add key="ImageBaseUrl" value="~/Content/Images/" /> <!--For Development-->
   <add key="ImageBaseUrl" value="https://d209523005EXAMPLE.cloudfront.net/Content/Images/" /> <!--For Production-->
</appSettings>