As mentioned in the HRM, the external pull-downs for the LP_CLK and LP_ACK pins is used so that the linkport can enable the transmitter and receiver, irrespective of the state of the other. We would not recommend using Internal pull down for them.
The internal pull down will not be a reliable solution and the purpose of the Internal pull down is required for keeping the pin in defined state.
Though, internal pull downs might work but those are generally to keep a pin in a defined state rather than a floating state.
In the context of protocol's perspective, this would not be recommended as the expected system behavior cannot be ensured.