This is a relatively easy one to fix. When you want to render/output the content you need to apply the metafield_tag filter to it.
In liquid this is just:
{{ RTE_METAFIELD_REFERENCE | metafield_tag }}
to output it. If you need it as a variable you can use the following (or you can capture it):
{% assign VARIABLE_NAME = RTE_METAFIELD_REFERENCE | metafield_tag %}
You won’t be able to do anything with these fields without delving into a bit of template modification.