I've observed a start-up overvoltage in LTspcie.
I've tried increase output capacitor, reduce load, delete LC filter etc.. But the overvoltage is always present.
Try to use the test jig of LTSpice for the simulation of LTM4661 and change the input and load conditions according to your needs. Kindly refer to page 8 of the datasheet for the output voltage programming. We have also tried to test this in an actual DC2569A demo board using the input voltage and output load conditions that you have provided in the schematic. The output voltage is plotted in the figure below. As you notice, there is very little to no overshoot (or overvoltage) seen in the output.