Given the disparate concerns, I think it best to divide them logically.
For the laptop, I would suggest looking at a laptop case or laptop bag, since it sounds like you were otherwise transporting the laptop naked or wrapped in a sweatshirt. Being your primary work tool, it does warrant its own protection, irrespective of an ebike or automobile or airplane commute. Laptop cases are like phone cases, in that they stay attached to the machine whether opened or close, usually by straps around the bottom. Some laptop cases are hard sized, and thus offer a lot of physical protection.
But a laptop bag would work equally well, such as those which look like messenger bags. Such soft sided bags offer less protection than a hard sided case to impacts, but they often are water/rain resistant when the bag is zipped up or the flap is laid over the top. I personally use a messenger bag with a laptop compartment, so I can carry my other work tools, like pen and paper, phone charger, and meeting headphones, whether I'm commuting to the office by car, bike, or walking.
In all circumstances, this layer of protection is bidirectional, preventing the laptop from sustaining damage but also protecting your panniers from holes. So now we get to panniers. Ideally, your laptop case/bag should fit into the pannier, and the pannier would be waterproof. This augments the rain resistancd of the laptop bag, while being flexible for other non-laptop payloads like groceries when you're not commuting.
Since you mentioned transporting other electronics as well as lunch, a dual pannier setup can make sense, where you laptop case/bag plus electronics are on one side, and lunch on the other. I do carry dual panniers on my acoustic bike, and it's terrible convenient when I don't want my payloads to unbalance the bike.
For rain clothes, presumably you would be wearing these while commuting? Do these need to be stored in the panniers? Or would this be in preparation for a rainy commute on the way back home? I personally prefer rain gear that I can shed anywhere, so I use breathable snow pants that still function in the dry, and a windbreaker than isn't too cumbersome to wear even if it isn't raining.
My bike tools are stored in an undersaddle bag which never leaves the bike. This means I need them to be fairly compact, but I do keep the essentials on me wherever I may run into trouble.
I think the key thing to remember with a bicycle commute -- electric or otherwise -- is that things will bounce around. It's not like in a car where something can be placed in the passenger footwell and it'll mostly get to the destination in one piece. No, stuff in panniers will bump into things, the side walls, and sometimes even try to escape out the top. Things like bike tools won't care about that, but electronics can be marred or damaged. Fortunately, this can be really easy to manage, with the simplest solution being a reusable grocery bag that you can tie shut. This clumps all the things together, so while the whole clump can still bounce around inside the pannier, they won't smash into each other. A step up would be some kind of padded bag, like what's used to transport cameras, with movable walls.
I wish you good luck in optimizing your bike commute! Don't be afraid to try stuff out and do test things to their limits so you have confidence that it'll serve you under all inclement conditions.