The ECO is needed to provide an accurate BLE frequencies +/- 100ppm or less. BLE frequencies need this accuracy or the other end of the BLE connection will not connect reliably. The WCO is potentially not necessary depending on the BLE message mode you are using. It is necessary for many of the BLE message modes which require +/-100ppm accuracy.
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The BLE ECO is mandatory for BLE functionality, and BLE ECO is already mounted inside CYBLE-416045-02. The ECO is different from the BLE ECO. They have different IO pins.
However, the main system clock can be sourced from BLE ECO if it's already there, therefore, the ECO could be omitted in this case.
As for the WCO, you need connect it outside the module.
That's the reason you may see Y1 is not loaded and Y2 is there on CY8CPROTO-063-BLE board.