htmltidy filter destroys tokens

I have question why is the media module using tokens (json [[]]) and media wrappers (<!--MEDIA-WRAPPER-START etc)? why not a simple img element?

First the media wrappers are sometimes generating a mess. This can deleting part of the text when the wrapper are converted to tokens. I fixed this with:

    /**
     * Replaces the placeholders for html editing with the media tokens to store.
     * @param {string} content
     */
    replacePlaceholderWithToken: function(content) {
      var tagmap = Drupal.media.filter.ensure_tagmap();
      var i = 1,
          expression,
          result;
      for (var macro in tagmap) {

        var startTag = Drupal.media.filter.getWrapperStart(i), endTag = Drupal.media.filter.getWrapperEnd(i);
        var startPos = content.indexOf(startTag), endPos = content.indexOf(endTag);
        if (startPos !== -1 && endPos !== -1) {
          // If the placeholder wrappers are empty, remove the macro too.
          if (endPos - startPos - startTag.length === 0) {
            macro = '';
          }

          // Check if there are placeholders inside this wrapped html, replace those first
          var html = content.substring(startPos + startTag.length, endPos);
          if (html.indexOf('<--MEDIA-WRAPPER-START') > 0) {
              html = this.replacePlaceholderWithToken(html);
              content = content.substr(0, startPos + startTag.length) + html + content.substr(endPos);
              return this.replacePlaceholderWithToken(content);
          }

          // Restore everything that is typed before the img tag or after the img tag
          expression = RegExp(startTag + '(.*)<img[^>]*>(.*)' + endTag);
          result = expression.exec(content);
          if (result && result.length === 3) {
              macro = result[1]  + macro + result[2];
          }
          content = content.substr(0, startPos) + macro + content.substr(endPos + (new String(endTag)).length);
        }
        i++;
      }

      // Don't let media placeholders bungle around, remove them.
      content = content.replace(/<!--MEDIA-WRAPPER-(START|END)-\d*-->/g, '');
      return content;
    },

but when i turned on the module 'htmltidy' the token ([[]]) get scrambled by entitlements, so the filter from the media module cannot convert it back to a <img> element.

I fixed this to remove the token/placeholders functionality code like this:

    /**
     * Replaces media tokens with the placeholders for html editing.
     * @param content
     */
    replaceTokenWithPlaceholder: function(content) {
      return content;
    },

    /**
     * Replaces the placeholders for html editing with the media tokens to store.
     * @param content
     */
    replacePlaceholderWithToken: function(content) {
      return content;
    },

Is there any other solution out there? because my solution feels bad. And why are the tokens saved in the database and not the wrapped html?