I understand the design choice to whitelist a specific list of common templates (Artwork, Photograph, etc.), but advanced users have valid use cases for using a custom template.
The most important one in my eyes is the use of ingestion templates, as they allow easily to do super-advanced formatting & metadata ingestion in plain wikitext − a method very popular with batch uploaders at the moment.
I realise this sort of defeats one of the purposes of the GWToolset − to map metadata − but it is very frustrating not being able to use the full power of wikitext for mapping.
(See https://commons.wikimedia.org/wiki/Commons:Mus%C3%A9e_des_Augustins/Ingestion for an example of such a template)