The cargo aircraft can dock at a spidertron docking station, which means they can transfer 20 slots of cargo very quickly, and do not require any waterways to use so they're much easier to set up. Is this intended? They are quite a bit more expensive I suppose.

They aren't meant to replace ships, no, but they are very strong, possibly too strong. They can carry 20, which is a lot less than cargo ships' 100, and they can't carry containers.

They are intended to be used for things that you only need small amounts of, things that you need to deliver to lots of places (e.g. ammo) and things that can't be containerised (such as building materials, repair packs). Maybe I need to drastically increase the fuel consumption?

Oh if they can't carry filled containers then you can't really compare them to ships after all and they're fine. Containers are 10x more slot-efficient so it's 20 slots vs effectively 1000, and cargo aircraft sure aren't 50x faster. They're more like an alternative to long range delivery drones.

Yep exactly. You can manually load them with containers since there’s no easy way for mods to prevent this, but I’ve made it so that docks can’t be used to automatically load filled containers onto spidertrons and aircraft.