In the doc:

https://docs.safe.com/fme/html/FME_Desktop_Documentation/FME_ReadersWriters/citygml/citygml.htm?Highlight=citygml

The part where the limitations are listed:

The CityGML reader reads all parts of the Thematic and Appearance CityGML models with the exception of the Digital Terrain Models (DTMs) ImplicitGeometry and xlink:href resolution.

is not really clear. Is there a comma after '(DTMs)'? Or do ImplicitGeometry are not read? (They are, I just tested!). Same for XLinks, they seem to be resolved (at least those internal to the file).