I've jacked up multiple vehicles (including a Leaf) hundreds of times at the factory jack points without causing structural or paint/undercoating damage.
I use a couple hockey pucks to provide a bit of cushion and avoid metal-on-metal contact. I've seen other folks cut a groove in a hockey puck, or in short block of wood, for the same purpose. You can also buy commercial products that do the same thing - basically a big chunk of dense rubber with a slot for the sill.
If you're jacking up the car from level ground, as you will be if you're using a commercial-style lift, you should be fine with the sill plate. It's made for lifting the car. If you're concerned about the car shifting on the lift plates then using a block that sort of grips the sill may provide additional confidence.