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Cultivators in the Spirit Stream Realm can only fly using Flying Spirit Artifacts, but once they reach the Cloud River Realm, they're able to fly through the air using their bodies alone.
The two concepts are different, one involves wielding a Flying Spirit Artifact and being carried by it, while the other relies on the physical body to fly directly.
Although Lu Ye is currently relying on wings spirit runes, he can somewhat be said to experience the benefits of flying through the air in advance.
Of course, that doesn't mean cultivators no longer need Flying Spirit Artifacts after reaching the Cloud River Realm, as flying with artifacts consumes less energy. Moreover, some Flying Spirit Artifacts can be fitted with Spirit Stones and other consumables to replace the cultivator's own spirit force.