Sorry to bump this thread out of the ground.
To have markdown rendered within HTML blocks, what is usually done in other Markdown dialects is to add a markdown=1 option in the html outer tag. An other solution retained in Github Flavoured Markdown is to add blank lines this way:
<div>
*Emphasized* text.
</div>
This kind of behaviour is currently what I need to render a gallery. I am doing it this way:
<div class="gallery" markdown=1>

:
<p class="p2">
{{ .Inner | .Page.RenderString }}
</p>
Markdown:
{{< biblio-ref >}}
Greely, Fred, Mary Jones, and Greg Attiks. *There's a Bat in My Barn: Struggles with the New Hampshire Brown Bat*. Wildlife Press, 2012.
{{< /biblio-ref >}}
Result: