Can the LTC3643 limit the supercapacitor charging current separately from the system load current?

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Accepted Answer

No, the LTC3643 cannot independently limit the supercapacitor charging current but its maximum charge current is 2A. 
 The input current limit—set by a sense resistor between the CLP and VIN pins—applies to the total current drawn by both the system load and the supercapacitor. 
 In the case of current limited power supply, the LTC3643 has a capability of limiting the input current of the boost regulator to ensure that the total current of the boost regulator and the system load does not exceed to the programmed amount.

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LTC3643: FAQ