So we are planning on having atmosphere affect the capabilities of towing? A tractor beam doesn't just suddenly negate the effects of gravity?

It doesn't negate the effects of gravity. It's a weird thing. One of Chris's big things is everything in the world and the universe is physicalized. It has real-world parameters. So whilst tractor beams do mitigate that to an extent, it doesn't make your ship suddenly become weightless. You're still having to do stuff in atmosphere with your own ship, and you're just connecting yourself to the other ship.