True - but then such intermediates are of no relevance to the question of transitions. If one were interested in a gradual transition in cranial capacity from Homo erectus to Homo sapiens, it would be of no interest that one species of Australapithecine had an intermediate cranial capacity.
In the case of the giraffe, we know that living okapis have short necks and living giraffes have long necks. We also know that fossil giraffes older than Samotherium major had necks as long as today’s. Some taxonomists even suggest that the earliest true giraffes may fall within the range of the present species. And that long and short necked forms coexisted for millions of years.
So the presence of a not-quite-so-short neck in one species of Samotherium gives no indication whatsoever that that trait existed at its divergence from the giraffes several million years before. Given the shorter necks of other, older, species in the Samotherium genus, in fact, it makes it vanishingly unlikely.