Custom block formats for preprocessed shortcode in TinyMCE

I’m trying to extend TinyMCE with some custom formats and I’ve got that working as per http://codex.ww.wp.xz.cn/TinyMCE_Custom_Styles#Using_style_formats

Basically my custom format is configured like this:

'title'   => 'Medium Left',
'block'   => 'div',
'classes' => 'article-special article-special-left article-special-medium',
'wrapper' => true

It works fine for everything but elements with processed shortcodes e.g. [caption]. As you know [caption] in the editor looks like this:

<div class="mceTemp">
  <dl ...>
    <dt ...>
      <a ...><img ...></a>
    </dt>
    <dd ...>caption</dd>
  </dl>
</div>

The behavior when selecting a custom format for a block element is described as:

Existing block elements within the selection gets replaced with the new block element.

So when the [caption] element is selected in the TinyMCE editor and I choose my custom format to apply to it I gets added to the outer-most <div class="mceTemp"> like this:

<div class="mceTemp article-special article-special-left article-special-medium">
  <dl ...>
    <dt ...>
      <a ...><img ...></a>
    </dt>
    <dd ...>caption</dd>
  </dl>
</div>

On save TinyMCE ignores the mceTemp div so the end result is as if I didn’t apply my custom format.

Now if I insert an image without caption then apply my custom format and add the caption in the end, all is fine. But that’s not a workflow I want to enforce.

How can I solve this? I’m working on WP 3.9.1.