Byzantium is just the continuation of the eastern part of the Roman Empire, so when did we start considering it to be its own political entity, completely different from the Roman Empire itself?
I have some previous answers that may be helpful:
In general we could say people in Latin western Europe stopped considering it the true empire by the late 8th century, when the empress Irene overthrew her son. In the west Charlemagne and the pope decided to "restore" the western empire by crowning Charlemagne emperor in 800.
But as for why modern historians call it "Byzantium", that is also confusing and complicated and one single answer doesn't really do it justice, but I have another answer that might help: