It is said that since one of the incarnations of Tulku Dragpa Gyeltsen was Dultzin Dragpa; and since Dultzin was regarded to have the same mind stream as Je Tsongkhapa and ultimately of Manjushri, Je Tsongkhapa's early studies and to me even his later works were of Manjushri's.
Having said that, the main thing here for me is that since Dorje Shugden manifested from this lineage as a Protector; and protectors; especially Dorje Shugden are known to be closer to beings because in the case of Dorje Shugden He manifested in the form of a samsaric god, then Manjushri's teaching as made suitable for us of these times by Je Tsongkhapa has never been closer and more available to beings.
Hence, this is the biggest opportunity for us. Don't act like the merchant who went to an island of jewels and came back empty handed.