In principle, the BT3554 measures the internal resistance and voltage of batteries by applying a 1kHz signal. It is best used for monitoring the state of batteries over time in order to determine the battery's state of health (SOH) by analyzing the changes in internal resistance.
In terms of measurement, yes, the BT3554 can measure the internal resistance of Li-ion batteries; however, the results will include the resistance of the protection circuit that is needed to maintain the voltage and current within safe limits in an LIB.
In addition, Li-ion batteries exhibit a very small change of internal resistance despite battery degradation or deterioration. Since the battery degradation is determined by the battery's change in internal resistance, the relatively small changes of this characteristic in an LIB will prevent the BT3554 from providing the robust data necessary to judge the battery's deterioration state.