I see the support has changed recently, but I just wanted to report a problem that could be handled more elegantly.
The Help tab of the Titles & Metas section says I can use %%ct_desc_<custom-tax-name>%% which is "Replaced with a custom taxonomoies description".
So, using the Easy Digital Downloads plugin which creates the "download" post type and the "download_category" and "download_tag" taxonomies, I put %%ct_desc_download_category%% in the box for the Meta description template on the Taxonomies tab under the Categories taxonomy (not the post category, but the download category).
With this in place, the plugin dies on the meta description line when I click on a taxonomy link. No error is logged (that I could see) and it looks like a blank page, but viewing the source of the page shows it stopped on the meta description tag.
Changing %%ct_desc_download_category%% to %%term_description%% works perfectly.