Right now, there is no ideal configuration to store a Custom Transformer exactly one time and use it within FME Desktop and FME Server as a Linked Custom Transformer. There are several workarounds:
1. Create Shared FME Folder --> use the folder within the Workbench --> upload Custom Transformers to FME Server
This works, but in fact it duplicates the Custom Transformer on each FME Server (Development, Staging, Production). When creating a new version of the Custom Transformer, it has to be uploaded to all FME Servers again.
2. Create network share and reference it as a Custom Resource within FME Server
Unfortunately, the FME Server Engine doesn't scan Custom Resources, so a Workspace with a Linked Custom Transformer from the network share will crash in FME Server.
3. Share the Engine Resource Folder of FME Server
This would also work, but I don't like the idea of exposing some server internal folder by sharing it to the network. Furthermore, it doesn't solve the problem of sharing a Custom Transformer across different FME Servers (Development, Staging, Production), because each instance would have its own Engine Resource Folder which would lead to multiple Shared FME Folders within Workbench.
4. Use Embedded Custom Transformers
Not really an option because it is impossible to use exactly the same Custom Transformer per definition.
Thus, FME Server and Desktop should be able to reference any arbitrary network folder as a source for Custom Transformers.