Some of that may be tires. Your ebike has front suspension though, right? That helps. Suspension seats also make a world of difference, and is something I want to add soon. My bike is solid front to rear. I am just used to standing on the "pegs" like I do when riding my dual sport off road when I know I am going to take a hit to the nethers.
Hard tail with solid forks at higher speeds makes for a slightly more bumpy ride. This is why Darwin and many others prefer the wider/bigger tires, as they can help make up for it by absorbing more impacts. The other solution is to just get used to the hammering.