Documenteer has a lsst-pipelinetasks directive that works analogously to lsst-cmdlinetasks. However, it is not mentioned in either the module topic documentation nor in the package templates. As a result, tasks that get converted to PipelineTask will drop off the module documentation.
Add a lsst-pipelinetasks section to the template (possibly before lsst-cmdlinetasks, which is still relevant until the migration is complete) and update the developer guide to match. Updating the index.rst files of individual packages is out of scope for this issue.