There are multiple ways of doing things because there were never any protocols built into the standards. You use whatever ad-hoc "standard" your equipment implements.
Just based on the names, RTS/CTS would seem to be a natural fit. However, it's backwards from the needs that developed over time. These signals were created at a time when a terminal would batch-send a screen full of data, but the receiver might not be ready, thus the need for flow control. Later the problem would be reversed, as the terminal couldn't keep up with data coming from the host, but the RTS/CTS signals go the wrong direction - the interface isn't orthogonal, and there's no corresponding signals going the other way. Equipment makers adapted as best they could, including using the DTR and DSR signals.
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