The encapsulation type does not dictate the usage of clock rate. On a serial connection, one device must provide clocking. If you have a small lab configured with a P2P connection, you will notice that the cables will have a DTE<->DCE. The DCE side must provide the clocking and this device must have the clock rate.
In a full blown network when you employ a carrier for your WAN connection, the carrier often provides the clocking so the carrier becomes the DCE unit and you configure both of your CSUs as DTE devices.
Encapsulation enables the ability to provide some extra features. For instance, with PPP you get authentication and bandwidth aggregation with MultiLink PPP.
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