I personally would clip the pins, there’s only 5-6mm of clearance in the thinner portion of the board between the pcb and the bottom plate, and the single cell lipos listed are both 4mm thick. So you only have 1-2 mm of clearance, which the pins are 1-2mm above the pcb surface, which wouldn’t leave much room for that pad, but you might be able to squeeze it all in, but fit would be tight. Plus with lipos you always want to leave a little room for possible swelling (batterys should be replaced if they swell a lot), any excessive swelling might make that pad useless, and you really don’t want that lipo to get punctured...
To each their own, and everyone can do it as they please; but that’s how I would personally do it, just to ensure that everything was as safe as possible for my build. Last thing I want is a flaming CA66.