There are those of us who create workspaces as products/tools which are distributed to customers who themselves have FME.
In the development process it's nice to be able to split up parts of a workspace in to modules (linked custom transformers) which can be worked on independently - A very standard approach for developing with code.
Using this method makes working with FME together with git a little more easier to handle - changes can be made in separate branches and merged without conflicts.
There is a big downside to Linked Transformers which is that the end user experience is not as nice and requires additional work either by the customer or via another method to make sure all definitions of Linked Customer transformers are up-to-date. Better is to have the Linked custom transformers embedded prior to delivery.
Currently there is no method to embed custom transformers except to open the workspace and choose embed for every one. This is not an option for automated pipelines. A method to embed all Custom Transformers would really help.