It is a limitation. Referring to SA:
Currently there is no possibility to directly include child Custom Record entries in the printouts utilizing Advanced PDF/HTML Templates. This is being tracked under Enhancement 304767.
As an alternate solution it is possible to create a beforeLoad User Event Script that will search over the custom subrecord entries and get the results into a custom field as JSON object. Then the Freemarker can parse the custom field content and build a HTML table in the printout.
See the SAs