This initiation could be done because Shangpa sheltered Jonang and so they became lineage holders of this Tantra.
Well....not technically correct.
By the time of Taranatha, there was no institutional Shangpa lineage, you know. The Shangpa transmission existed in the Karma Kagyu institutions, the Sakya Institutions, etc. Jetsun Taranatha actually founded his own monastery, and it was identified as Jonang, institutionally, until it was forcibly taken by the Gelukpas at the time of the 5th Dalai Lama.
Taranatha also was, to a very great extent, the codifier of the "long lineage" of the Shangpa Kagyu (as well as being a master of most Sarma traditions--he was a LamDre practitioner as well...) so I think it's more appropriate to say that the Jonang "sheltered" the Shangpa.
Since the time of Taranatha, until now, there's really been no institutional "Shangpa"--Kongtrul Lodro Taye talks about obtaining the empowerments, and he propagated the lineage from within the Karma Kagyu institution--while Jamyang Khyentse Wangpo propagated it amongst the Sakya, mainly.