At the moment if you have a published parameter in Main workspace, you can't access it straight from an embedded custom transformer. You have to create a new published parameter in the custom transformer, and link the parameter in main view to the custom transformer's parameter. It would be nice to have Workspace Parameters or similar in the User Parameters section of the custom transformer's navigator.
Especially with embedded transformers I mostly clean up my workspace, but if I need to use 10 parameters of the main workspace inside the custom transformer, it's a hassle to create all the parameters again in the custom transformer.

