Hi Rik,
Welcome to the MPS Technical Forum. I can only answer questions specifically on MPS devices. For more information on Arduino products, please visit their website.
If you are planning to connect a 5V source to the output node of the MPM3610, even with Vin disconnected, I strongly advice against this. I am confused what you mean by “unloaded” when you saw the 5.46V on the input. Did you measure the input pin while driving the output with a separate 5V source? Have you done any testing with the MPM3610’s input and output completely isolated from the rest of the board?