SwitcherPro uses the transient load step and max voltage inputs to calculate an output impedance requirement for the converter, and correspondingly selects output capacitors to meet that requirement. From your description and the signficant change in load current and transient specifications you tried, I agree that the capacitance should be changing.
However, SwitcherPro is no longer in active development. The TPS40304 is in WEBENCH, and I suggest you use WEBENCH to create your design. For this particular device, the output capacitor is selected in WEBENCH to meet a 40% load current step with 2% transient step voltage max. I've verified that changing the load current from 2 to 12A in WEBENCH for a 12Vin-5Vout design does change the selected Cout from 20uF to 100uF. You can launch a TPS40304 WEBENCH design from the product page panel:
